2 !-----------------------------------------------------------------------------
15 !-----------------------------------------------------------------------------
17 ! common /mdgrad/ in module.energy
18 ! common /back_constr/ in module.energy
19 ! common /qmeas/ in module.energy
23 real(kind=8),dimension(:),allocatable :: d_t_work,&
24 d_t_work_new,d_af_work,d_as_work,kinetic_force !(MAXRES6)
25 real(kind=8),dimension(:,:),allocatable :: d_t_new,&
26 d_a_old,d_a_short!,d_a !(3,0:MAXRES2)
27 ! real(kind=8),dimension(:),allocatable :: d_a_work !(6*MAXRES)
28 ! real(kind=8),dimension(:,:),allocatable :: Gmat,Ginv,A,&
29 ! Gsqrp,Gsqrm,Gvec !(maxres2,maxres2)
30 ! real(kind=8),dimension(:),allocatable :: Geigen !(maxres2)
31 ! integer :: dimen,dimen1,dimen3
32 ! integer :: lang,count_reset_moment,count_reset_vel
33 ! logical :: reset_moment,reset_vel,rattle,RESPA
36 ! real(kind=8) :: rwat,etawat,stdfp,cPoise
37 ! real(kind=8),dimension(:),allocatable :: gamsc !(ntyp1)
38 ! real(kind=8),dimension(:),allocatable :: stdfsc !(ntyp)
39 real(kind=8),dimension(:),allocatable :: stdforcp,stdforcsc !(MAXRES)
40 !-----------------------------------------------------------------------------
44 ! ###################################################
45 ! ## COPYRIGHT (C) 1992 by Jay William Ponder ##
46 ! ## All Rights Reserved ##
47 ! ###################################################
49 ! #############################################################
51 ! ## sizes.i -- parameter values to set array dimensions ##
53 ! #############################################################
56 ! "sizes.i" sets values for critical array dimensions used
57 ! throughout the software; these parameters will fix the size
58 ! of the largest systems that can be handled; values too large
59 ! for the computer's memory and/or swap space to accomodate
60 ! will result in poor performance or outright failure
62 ! parameter: maximum allowed number of:
64 ! maxatm atoms in the molecular system
65 ! maxval atoms directly bonded to an atom
66 ! maxgrp ! user-defined groups of atoms
67 ! maxtyp force field atom type definitions
68 ! maxclass force field atom class definitions
69 ! maxkey lines in the keyword file
70 ! maxrot bonds for torsional rotation
71 ! maxvar optimization variables (vector storage)
72 ! maxopt optimization variables (matrix storage)
73 ! maxhess off-diagonal Hessian elements
74 ! maxlight sites for method of lights neighbors
75 ! maxvib vibrational frequencies
76 ! maxgeo distance geometry points
77 ! maxcell unit cells in replicated crystal
78 ! maxring 3-, 4-, or 5-membered rings
79 ! maxfix geometric restraints
80 ! maxbio biopolymer atom definitions
81 ! maxres residues in the macromolecule
82 ! maxamino amino acid residue types
83 ! maxnuc nucleic acid residue types
84 ! maxbnd covalent bonds in molecular system
85 ! maxang bond angles in molecular system
86 ! maxtors torsional angles in molecular system
87 ! maxpi atoms in conjugated pisystem
88 ! maxpib covalent bonds involving pisystem
89 ! maxpit torsional angles involving pisystem
92 !el integer maxatm,maxval,maxgrp
93 !el integer maxtyp,maxclass,maxkey
94 !el integer maxrot,maxopt
95 !el integer maxhess,maxlight,maxvib
96 !el integer maxgeo,maxcell,maxring
97 !el integer maxfix,maxbio
98 !el integer maxamino,maxnuc,maxbnd
99 !el integer maxang,maxtors,maxpi
100 !el integer maxpib,maxpit
101 ! integer :: maxatm !=2*nres !maxres2 maxres2=2*maxres
102 ! integer,parameter :: maxval=8
103 ! integer,parameter :: maxgrp=1000
104 ! integer,parameter :: maxtyp=3000
105 ! integer,parameter :: maxclass=500
106 ! integer,parameter :: maxkey=10000
107 ! integer,parameter :: maxrot=1000
108 ! integer,parameter :: maxopt=1000
109 ! integer,parameter :: maxhess=1000000
110 ! integer :: maxlight !=8*maxatm
111 ! integer,parameter :: maxvib=1000
112 ! integer,parameter :: maxgeo=1000
113 ! integer,parameter :: maxcell=10000
114 ! integer,parameter :: maxring=10000
115 ! integer,parameter :: maxfix=10000
116 ! integer,parameter :: maxbio=10000
117 ! integer,parameter :: maxamino=31
118 ! integer,parameter :: maxnuc=12
119 ! integer :: maxbnd !=2*maxatm
120 ! integer :: maxang !=3*maxatm
121 ! integer :: maxtors !=4*maxatm
122 ! integer,parameter :: maxpi=100
123 ! integer,parameter :: maxpib=2*maxpi
124 ! integer,parameter :: maxpit=4*maxpi
125 !-----------------------------------------------------------------------------
126 ! Maximum number of seed
127 ! integer,parameter :: max_seed=1
128 !-----------------------------------------------------------------------------
129 real(kind=8),dimension(:),allocatable :: stochforcvec !(MAXRES6) maxres6=6*maxres
130 ! common /stochcalc/ stochforcvec
131 !-----------------------------------------------------------------------------
132 ! common /przechowalnia/ subroutines: rattle1,rattle2,rattle_brown
133 real(kind=8),dimension(:,:),allocatable :: GGinv !(2*nres,2*nres) maxres2=2*maxres
134 real(kind=8),dimension(:,:,:),allocatable :: gdc !(3,2*nres,2*nres) maxres2=2*maxres
135 real(kind=8),dimension(:,:),allocatable :: Cmat !(2*nres,2*nres) maxres2=2*maxres
136 !-----------------------------------------------------------------------------
137 ! common /syfek/ subroutines: friction_force,setup_fricmat
138 !el real(kind=8),dimension(:),allocatable :: gamvec !(MAXRES6) or (MAXRES2)
139 !-----------------------------------------------------------------------------
140 ! common /przechowalnia/ subroutines: friction_force,setup_fricmat
141 real(kind=8),dimension(:,:),allocatable :: ginvfric !(2*nres,2*nres) !maxres2=2*maxres
142 !-----------------------------------------------------------------------------
143 ! common /przechowalnia/ subroutine: setup_fricmat
144 real(kind=8),dimension(:,:),allocatable :: fcopy !(2*nres,2*nres)
145 !-----------------------------------------------------------------------------
148 !-----------------------------------------------------------------------------
150 !-----------------------------------------------------------------------------
152 !-----------------------------------------------------------------------------
153 subroutine brown_step(itime)
154 !------------------------------------------------
155 ! Perform a single Euler integration step of Brownian dynamics
156 !------------------------------------------------
157 ! implicit real*8 (a-h,o-z)
159 use control, only: tcpu
162 ! use io_conf, only:cartprint
163 ! include 'DIMENSIONS'
167 ! include 'COMMON.CONTROL'
168 ! include 'COMMON.VAR'
169 ! include 'COMMON.MD'
171 ! include 'COMMON.LANGEVIN'
173 ! include 'COMMON.LANGEVIN.lang0'
175 ! include 'COMMON.CHAIN'
176 ! include 'COMMON.DERIV'
177 ! include 'COMMON.GEO'
178 ! include 'COMMON.LOCAL'
179 ! include 'COMMON.INTERACT'
180 ! include 'COMMON.IOUNITS'
181 ! include 'COMMON.NAMES'
182 ! include 'COMMON.TIME1'
183 real(kind=8),dimension(6*nres) :: zapas !(MAXRES6) maxres6=6*maxres
184 integer :: rstcount !ilen,
186 !el real(kind=8),dimension(6*nres) :: stochforcvec !(MAXRES6) maxres6=6*maxres
187 real(kind=8),dimension(6*nres,2*nres) :: Bmat,GBmat,Tmat !(MAXRES6,MAXRES2) (maxres2=2*maxres,maxres6=6*maxres)
188 real(kind=8),dimension(2*nres,2*nres) :: Cmat_,Cinv !(maxres2,maxres2) maxres2=2*maxres
189 real(kind=8),dimension(6*nres,6*nres) :: Pmat !(maxres6,maxres6) maxres6=6*maxres
190 ! real(kind=8),dimension(:,:),allocatable :: Bmat,GBmat,Tmat !(MAXRES6,MAXRES2) (maxres2=2*maxres,maxres6=6*maxres)
191 ! real(kind=8),dimension(:,:),allocatable :: Cmat_,Cinv !(maxres2,maxres2) maxres2=2*maxres
192 ! real(kind=8),dimension(:,:),allocatable :: Pmat !(maxres6,maxres6) maxres6=6*maxres
193 real(kind=8),dimension(6*nres) :: Td !(maxres6) maxres6=6*maxres
194 real(kind=8),dimension(2*nres) :: ppvec !(maxres2) maxres2=2*maxres
195 !el common /stochcalc/ stochforcvec
196 !el real(kind=8),dimension(3) :: cm !el
197 !el common /gucio/ cm
199 logical :: lprn = .false.,lprn1 = .false.
200 integer :: maxiter = 5
201 real(kind=8) :: difftol = 1.0d-5
202 real(kind=8) :: xx,diffmax,blen2,diffbond,tt0
203 integer :: i,j,nbond,k,ind,ind1,iter
204 integer :: nres2,nres6
208 ! if (.not.allocated(Bmat)) allocate(Bmat(nres6,nres2))
209 ! if (.not.allocated(GBmat)) allocate (GBmat(nres6,nres2))
210 ! if (.not.allocated(Tmat)) allocate (Tmat(nres6,nres2))
211 ! if (.not.allocated(Cmat_)) allocate(Cmat_(nres2,nres2))
212 ! if (.not.allocated(Cinv)) allocate (Cinv(nres2,nres2))
213 ! if (.not.allocated(Pmat)) allocate(Pmat(6*nres,6*nres))
215 if (.not.allocated(stochforcvec)) allocate(stochforcvec(nres6)) !(MAXRES6) maxres6=6*maxres
219 if (itype(i,1).ne.10) nbond=nbond+1
223 write (iout,*) "Generalized inverse of fricmat"
224 call matout(dimen,dimen,nres6,nres6,fricmat)
236 Bmat(ind+j,ind1)=dC_norm(j,i)
241 if (itype(i,1).ne.10) then
244 Bmat(ind+j,ind1)=dC_norm(j,i+nres)
250 write (iout,*) "Matrix Bmat"
251 call MATOUT(nbond,dimen,nres6,nres6,Bmat)
257 GBmat(i,j)=GBmat(i,j)+fricmat(i,k)*Bmat(k,j)
262 write (iout,*) "Matrix GBmat"
263 call MATOUT(nbond,dimen,nres6,nres2,Gbmat)
269 Cmat_(i,j)=Cmat_(i,j)+Bmat(k,i)*GBmat(k,j)
274 write (iout,*) "Matrix Cmat"
275 call MATOUT(nbond,nbond,nres2,nres2,Cmat_)
277 call matinvert(nbond,nres2,Cmat_,Cinv,osob)
279 write (iout,*) "Matrix Cinv"
280 call MATOUT(nbond,nbond,nres2,nres2,Cinv)
286 Tmat(i,j)=Tmat(i,j)+GBmat(i,k)*Cinv(k,j)
291 write (iout,*) "Matrix Tmat"
292 call MATOUT(nbond,dimen,nres6,nres2,Tmat)
302 Pmat(i,j)=Pmat(i,j)-Tmat(i,k)*Bmat(j,k)
307 write (iout,*) "Matrix Pmat"
308 call MATOUT(dimen,dimen,nres6,nres6,Pmat)
315 Td(i)=Td(i)+vbl*Tmat(i,ind)
318 if (itype(k,1).ne.10) then
320 Td(i)=Td(i)+vbldsc0(1,itype(k,1))*Tmat(i,ind)
325 write (iout,*) "Vector Td"
327 write (iout,'(i5,f10.5)') i,Td(i)
330 call stochastic_force(stochforcvec)
332 write (iout,*) "stochforcvec"
334 write (iout,*) i,stochforcvec(i)
338 zapas(j)=-gcart(j,0)+stochforcvec(j)
340 dC_work(j)=dC_old(j,0)
346 zapas(ind)=-gcart(j,i)+stochforcvec(ind)
347 dC_work(ind)=dC_old(j,i)
351 if (itype(i,1).ne.10) then
354 zapas(ind)=-gxcart(j,i)+stochforcvec(ind)
355 dC_work(ind)=dC_old(j,i+nres)
361 write (iout,*) "Initial d_t_work"
363 write (iout,*) i,d_t_work(i)
370 d_t_work(i)=d_t_work(i)+fricmat(i,j)*zapas(j)
377 zapas(i)=zapas(i)+Pmat(i,j)*(dC_work(j)+d_t_work(j)*d_time)
381 write (iout,*) "Final d_t_work and zapas"
383 write (iout,*) i,d_t_work(i),zapas(i)
397 dc_work(ind+j)=dc(j,i)
403 d_t(j,i+nres)=d_t_work(ind+j)
404 dc(j,i+nres)=zapas(ind+j)
405 dc_work(ind+j)=dc(j,i+nres)
411 write (iout,*) "Before correction for rotational lengthening"
412 write (iout,*) "New coordinates",&
413 " and differences between actual and standard bond lengths"
418 write (iout,'(i5,3f10.5,5x,f10.5,e15.5)') &
422 if (itype(i,1).ne.10) then
424 xx=vbld(i+nres)-vbldsc0(1,itype(i,1))
425 write (iout,'(i5,3f10.5,5x,f10.5,e15.5)') &
426 i,(dC(j,i+nres),j=1,3),xx
430 ! Second correction (rotational lengthening)
436 blen2 = scalar(dc(1,i),dc(1,i))
437 ppvec(ind)=2*vbl**2-blen2
438 diffbond=dabs(vbl-dsqrt(blen2))
439 if (diffbond.gt.diffmax) diffmax=diffbond
440 if (ppvec(ind).gt.0.0d0) then
441 ppvec(ind)=dsqrt(ppvec(ind))
446 write (iout,'(i5,3f10.5)') ind,diffbond,ppvec(ind)
450 if (itype(i,1).ne.10) then
452 blen2 = scalar(dc(1,i+nres),dc(1,i+nres))
453 ppvec(ind)=2*vbldsc0(1,itype(i,1))**2-blen2
454 diffbond=dabs(vbldsc0(1,itype(i,1))-dsqrt(blen2))
455 if (diffbond.gt.diffmax) diffmax=diffbond
456 if (ppvec(ind).gt.0.0d0) then
457 ppvec(ind)=dsqrt(ppvec(ind))
462 write (iout,'(i5,3f10.5)') ind,diffbond,ppvec(ind)
466 if (lprn) write (iout,*) "iter",iter," diffmax",diffmax
467 if (diffmax.lt.difftol) goto 10
471 Td(i)=Td(i)+ppvec(j)*Tmat(i,j)
477 zapas(i)=zapas(i)+Pmat(i,j)*dc_work(j)
488 dc_work(ind+j)=zapas(ind+j)
493 if (itype(i,1).ne.10) then
495 dc(j,i+nres)=zapas(ind+j)
496 dc_work(ind+j)=zapas(ind+j)
501 ! Building the chain from the newly calculated coordinates
504 if (large.and. mod(itime,ntwe).eq.0) then
505 write (iout,*) "Cartesian and internal coordinates: step 1"
508 write (iout,'(a)') "Potential forces"
510 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(-gcart(j,i),j=1,3),&
513 write (iout,'(a)') "Stochastic forces"
515 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(stochforc(j,i),j=1,3),&
516 (stochforc(j,i+nres),j=1,3)
518 write (iout,'(a)') "Velocities"
520 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),&
521 (d_t(j,i+nres),j=1,3)
526 write (iout,*) "After correction for rotational lengthening"
527 write (iout,*) "New coordinates",&
528 " and differences between actual and standard bond lengths"
533 write (iout,'(i5,3f10.5,5x,f10.5,e15.5)') &
537 if (itype(i,1).ne.10) then
539 xx=vbld(i+nres)-vbldsc0(1,itype(i,1))
540 write (iout,'(i5,3f10.5,5x,f10.5,e15.5)') &
541 i,(dC(j,i+nres),j=1,3),xx
546 ! write (iout,*) "Too many attempts at correcting the bonds"
554 ! Calculate energy and forces
556 call etotal(potEcomp)
557 potE=potEcomp(0)-potEcomp(20)
561 ! Calculate the kinetic and total energy and the kinetic temperature
564 t_enegrad=t_enegrad+MPI_Wtime()-tt0
566 t_enegrad=t_enegrad+tcpu()-tt0
569 kinetic_T=2.0d0/(dimen*Rb)*EK
571 end subroutine brown_step
572 !-----------------------------------------------------------------------------
574 !-----------------------------------------------------------------------------
575 subroutine gauss(RO,AP,MT,M,N,*)
577 ! CALCULATES (RO**(-1))*AP BY GAUSS ELIMINATION
578 ! RO IS A SQUARE MATRIX
579 ! THE CALCULATED PRODUCT IS STORED IN AP
580 ! ABNORMAL EXIT IF RO IS SINGULAR
582 integer :: MT, M, N, M1,I,J,IM,&
584 real(kind=8) :: RO(MT,M),AP(MT,N),X,RM,PR,Y
590 if(dabs(X).le.1.0D-13) return 1
602 if(DABS(RO(J,I)).LE.RM) goto 2
616 if(dabs(X).le.1.0E-13) return 1
625 8 AP(J,K)=AP(J,K)-Y*AP(I,K)
627 9 RO(J,K)=RO(J,K)-Y*RO(I,K)
631 if(dabs(X).le.1.0E-13) return 1
641 15 X=X-AP(K,J)*RO(MI,K)
646 !-----------------------------------------------------------------------------
648 !-----------------------------------------------------------------------------
649 subroutine kinetic(KE_total)
650 !----------------------------------------------------------------
651 ! This subroutine calculates the total kinetic energy of the chain
652 !-----------------------------------------------------------------
654 ! implicit real*8 (a-h,o-z)
655 ! include 'DIMENSIONS'
656 ! include 'COMMON.VAR'
657 ! include 'COMMON.CHAIN'
658 ! include 'COMMON.DERIV'
659 ! include 'COMMON.GEO'
660 ! include 'COMMON.LOCAL'
661 ! include 'COMMON.INTERACT'
662 ! include 'COMMON.MD'
663 ! include 'COMMON.IOUNITS'
664 real(kind=8) :: KE_total,mscab
666 integer :: i,j,k,iti,mnum
667 real(kind=8) :: KEt_p,KEt_sc,KEr_p,KEr_sc,incr(3),&
670 write (iout,*) "Velocities, kietic"
672 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),&
673 (d_t(j,i+nres),j=1,3)
678 ! write (iout,*) "ISC",(isc(itype(i,1)),i=1,nres)
679 ! The translational part for peptide virtual bonds
685 if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
686 ! write (iout,*) "Kinetic trp:",i,(incr(j),j=1,3)
688 v(j)=incr(j)+0.5d0*d_t(j,i)
690 vtot(i)=v(1)*v(1)+v(2)*v(2)+v(3)*v(3)
691 KEt_p=KEt_p+mp(mnum)*(v(1)*v(1)+v(2)*v(2)+v(3)*v(3))
693 incr(j)=incr(j)+d_t(j,i)
696 ! write(iout,*) 'KEt_p', KEt_p
697 ! The translational part for the side chain virtual bond
698 ! Only now we can initialize incr with zeros. It must be equal
699 ! to the velocities of the first Calpha.
705 iti=iabs(itype(i,mnum))
711 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
712 if (itype(i,1).eq.10 .or. itype(i,mnum).eq.ntyp1_molec(mnum)&
713 .or.(mnum.eq.5)) then
719 v(j)=incr(j)+d_t(j,nres+i)
722 ! write (iout,*) "Kinetic trsc:",i,(incr(j),j=1,3)
723 ! write (iout,*) "i",i," msc",msc(iti)," v",(v(j),j=1,3)
724 KEt_sc=KEt_sc+mscab*(v(1)*v(1)+v(2)*v(2)+v(3)*v(3))
725 vtot(i+nres)=v(1)*v(1)+v(2)*v(2)+v(3)*v(3)
727 incr(j)=incr(j)+d_t(j,i)
731 ! write(iout,*) 'KEt_sc', KEt_sc
732 ! The part due to stretching and rotation of the peptide groups
736 ! write (iout,*) "i",i
737 ! write (iout,*) "i",i," mag1",mag1," mag2",mag2
741 ! write (iout,*) "Kinetic rotp:",i,(incr(j),j=1,3)
742 KEr_p=KEr_p+Ip(mnum)*(incr(1)*incr(1)+incr(2)*incr(2) &
746 ! write(iout,*) 'KEr_p', KEr_p
747 ! The rotational part of the side chain virtual bond
751 iti=iabs(itype(i,mnum))
752 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
753 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
754 .and.(mnum.ne.5)) then
756 incr(j)=d_t(j,nres+i)
758 ! write (iout,*) "Kinetic rotsc:",i,(incr(j),j=1,3)
759 KEr_sc=KEr_sc+Isc(iti,mnum)*(incr(1)*incr(1)+incr(2)*incr(2)+ &
763 ! The total kinetic energy
765 ! write(iout,*) 'KEr_sc', KEr_sc
766 KE_total=0.5d0*(KEt_p+KEt_sc+0.25d0*KEr_p+KEr_sc)
767 ! write (iout,*) "KE_total",KE_total
769 end subroutine kinetic
770 !-----------------------------------------------------------------------------
772 !-----------------------------------------------------------------------------
774 !------------------------------------------------
775 ! The driver for molecular dynamics subroutines
776 !------------------------------------------------
779 use control, only:tcpu,ovrtim
780 ! use io_comm, only:ilen
782 use compare, only:secondary2,hairpin
783 use io, only:cartout,statout
784 ! implicit real*8 (a-h,o-z)
785 ! include 'DIMENSIONS'
788 integer :: IERROR,ERRCODE
790 ! include 'COMMON.SETUP'
791 ! include 'COMMON.CONTROL'
792 ! include 'COMMON.VAR'
793 ! include 'COMMON.MD'
795 ! include 'COMMON.LANGEVIN'
797 ! include 'COMMON.LANGEVIN.lang0'
799 ! include 'COMMON.CHAIN'
800 ! include 'COMMON.DERIV'
801 ! include 'COMMON.GEO'
802 ! include 'COMMON.LOCAL'
803 ! include 'COMMON.INTERACT'
804 ! include 'COMMON.IOUNITS'
805 ! include 'COMMON.NAMES'
806 ! include 'COMMON.TIME1'
807 ! include 'COMMON.HAIRPIN'
808 real(kind=8),dimension(3) :: L,vcm
810 real(kind=8),dimension(6*nres) :: v_work,v_transf !(maxres6) maxres6=6*maxres
812 integer :: rstcount !ilen,
814 character(len=50) :: tytul
815 !el common /gucio/ cm
816 integer :: itime,i,j,nharp
817 integer,dimension(4,nres/3) :: iharp !(4,nres/3)(4,maxres/3)
819 real(kind=8) :: tt0,scalfac
825 print *,"MY tmpdir",tmpdir,ilen(tmpdir)
826 if (ilen(tmpdir).gt.0) &
827 call copy_to_tmp(pref_orig(:ilen(pref_orig))//"_" &
828 //liczba(:ilen(liczba))//'.rst')
830 if (ilen(tmpdir).gt.0) &
831 call copy_to_tmp(pref_orig(:ilen(pref_orig))//"_"//'.rst')
838 write (iout,'(20(1h=),a20,20(1h=))') "MD calculation started"
844 print *,"just befor setup matix",nres
845 ! Determine the inverse of the inertia matrix.
846 call setup_MD_matrices
848 print *,"AFTER SETUP MATRICES"
850 print *,"AFTER INIT MD"
853 t_MDsetup = MPI_Wtime()-tt0
855 t_MDsetup = tcpu()-tt0
858 ! Entering the MD loop
864 if (lang.eq.2 .or. lang.eq.3) then
868 call sd_verlet_p_setup
870 call sd_verlet_ciccotti_setup
874 pfric0_mat(i,j,0)=pfric_mat(i,j)
875 afric0_mat(i,j,0)=afric_mat(i,j)
876 vfric0_mat(i,j,0)=vfric_mat(i,j)
877 prand0_mat(i,j,0)=prand_mat(i,j)
878 vrand0_mat1(i,j,0)=vrand_mat1(i,j)
879 vrand0_mat2(i,j,0)=vrand_mat2(i,j)
884 flag_stoch(i)=.false.
888 "LANG=2 or 3 NOT SUPPORTED. Recompile without -DLANG0"
890 call MPI_Abort(MPI_COMM_WORLD,IERROR,ERRCODE)
894 else if (lang.eq.1 .or. lang.eq.4) then
895 print *,"before setup_fricmat"
897 print *,"after setup_fricmat"
900 t_langsetup=MPI_Wtime()-tt0
903 t_langsetup=tcpu()-tt0
906 do itime=1,n_timestep
908 if (large.and. mod(itime,ntwe).eq.0) &
909 write (iout,*) "itime",itime
911 if (lang.gt.0 .and. surfarea .and. &
912 mod(itime,reset_fricmat).eq.0) then
913 if (lang.eq.2 .or. lang.eq.3) then
917 call sd_verlet_p_setup
919 call sd_verlet_ciccotti_setup
923 pfric0_mat(i,j,0)=pfric_mat(i,j)
924 afric0_mat(i,j,0)=afric_mat(i,j)
925 vfric0_mat(i,j,0)=vfric_mat(i,j)
926 prand0_mat(i,j,0)=prand_mat(i,j)
927 vrand0_mat1(i,j,0)=vrand_mat1(i,j)
928 vrand0_mat2(i,j,0)=vrand_mat2(i,j)
933 flag_stoch(i)=.false.
936 else if (lang.eq.1 .or. lang.eq.4) then
939 write (iout,'(a,i10)') &
940 "Friction matrix reset based on surface area, itime",itime
942 if (reset_vel .and. tbf .and. lang.eq.0 &
943 .and. mod(itime,count_reset_vel).eq.0) then
945 write(iout,'(a,f20.2)') &
946 "Velocities reset to random values, time",totT
949 d_t_old(j,i)=d_t(j,i)
953 if (reset_moment .and. mod(itime,count_reset_moment).eq.0) then
957 d_t(j,0)=d_t(j,0)-vcm(j)
960 kinetic_T=2.0d0/(dimen3*Rb)*EK
961 scalfac=dsqrt(T_bath/kinetic_T)
962 write(iout,'(a,f20.2)') "Momenta zeroed out, time",totT
965 d_t_old(j,i)=scalfac*d_t(j,i)
971 ! Time-reversible RESPA algorithm
972 ! (Tuckerman et al., J. Chem. Phys., 97, 1990, 1992)
973 call RESPA_step(itime)
975 ! Variable time step algorithm.
976 call velverlet_step(itime)
980 call brown_step(itime)
982 print *,"Brown dynamics not here!"
984 call MPI_Abort(MPI_COMM_WORLD,IERROR,ERRCODE)
990 if (mod(itime,ntwe).eq.0) then
993 ! call check_ecartint
1003 v_work(ind)=d_t(j,i)
1008 if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1.and.mnum.ne.5) then
1011 v_work(ind)=d_t(j,i+nres)
1016 write (66,'(80f10.5)') &
1017 ((d_t(j,i),j=1,3),i=0,nres-1),((d_t(j,i+nres),j=1,3),i=1,nres)
1021 v_transf(i)=v_transf(i)+gvec(j,i)*v_work(j)
1023 v_transf(i)= v_transf(i)*dsqrt(geigen(i))
1025 write (67,'(80f10.5)') (v_transf(i),i=1,ind)
1028 if (mod(itime,ntwx).eq.0) then
1030 write (tytul,'("time",f8.2)') totT
1032 call hairpin(.true.,nharp,iharp)
1033 call secondary2(.true.)
1034 call pdbout(potE,tytul,ipdb)
1039 if (rstcount.eq.1000.or.itime.eq.n_timestep) then
1040 open(irest2,file=rest2name,status='unknown')
1041 write(irest2,*) totT,EK,potE,totE,t_bath
1043 ! AL 4/17/17: Now writing d_t(0,:) too
1045 write (irest2,'(3e15.5)') (d_t(j,i),j=1,3)
1047 ! AL 4/17/17: Now writing d_c(0,:) too
1049 write (irest2,'(3e15.5)') (dc(j,i),j=1,3)
1057 t_MD=MPI_Wtime()-tt0
1061 write (iout,'(//35(1h=),a10,35(1h=)/10(/a40,1pe15.5))') &
1063 'MD calculations setup:',t_MDsetup,&
1064 'Energy & gradient evaluation:',t_enegrad,&
1065 'Stochastic MD setup:',t_langsetup,&
1066 'Stochastic MD step setup:',t_sdsetup,&
1068 write (iout,'(/28(1h=),a25,27(1h=))') &
1069 ' End of MD calculation '
1071 write (iout,*) "time for etotal",t_etotal," elong",t_elong,&
1073 write (iout,*) "time_fric",time_fric," time_stoch",time_stoch,&
1074 " time_fricmatmult",time_fricmatmult," time_fsample ",&
1079 !-----------------------------------------------------------------------------
1080 subroutine velverlet_step(itime)
1081 !-------------------------------------------------------------------------------
1082 ! Perform a single velocity Verlet step; the time step can be rescaled if
1083 ! increments in accelerations exceed the threshold
1084 !-------------------------------------------------------------------------------
1085 ! implicit real*8 (a-h,o-z)
1086 ! include 'DIMENSIONS'
1088 use control, only:tcpu
1092 integer :: ierror,ierrcode
1093 real(kind=8) :: errcode
1095 ! include 'COMMON.SETUP'
1096 ! include 'COMMON.VAR'
1097 ! include 'COMMON.MD'
1099 ! include 'COMMON.LANGEVIN'
1101 ! include 'COMMON.LANGEVIN.lang0'
1103 ! include 'COMMON.CHAIN'
1104 ! include 'COMMON.DERIV'
1105 ! include 'COMMON.GEO'
1106 ! include 'COMMON.LOCAL'
1107 ! include 'COMMON.INTERACT'
1108 ! include 'COMMON.IOUNITS'
1109 ! include 'COMMON.NAMES'
1110 ! include 'COMMON.TIME1'
1111 ! include 'COMMON.MUCA'
1112 real(kind=8),dimension(3) :: vcm,incr
1113 real(kind=8),dimension(3) :: L
1114 integer :: count,rstcount !ilen,
1116 character(len=50) :: tytul
1117 integer :: maxcount_scale = 20
1118 !el common /gucio/ cm
1119 !el real(kind=8),dimension(6*nres) :: stochforcvec !(MAXRES6) maxres6=6*maxres
1120 !el common /stochcalc/ stochforcvec
1121 integer :: itime,icount_scale,itime_scal,i,j,ifac_time
1123 real(kind=8) :: epdrift,tt0,fac_time
1125 if (.not.allocated(stochforcvec)) allocate(stochforcvec(6*nres)) !(MAXRES6) maxres6=6*maxres
1131 else if (lang.eq.2 .or. lang.eq.3) then
1133 call stochastic_force(stochforcvec)
1136 "LANG=2 or 3 NOT SUPPORTED. Recompile without -DLANG0"
1138 call MPI_Abort(MPI_COMM_WORLD,IERROR,ERRCODE)
1145 icount_scale=icount_scale+1
1146 if (icount_scale.gt.maxcount_scale) then
1148 "ERROR: too many attempts at scaling down the time step. ",&
1149 "amax=",amax,"epdrift=",epdrift,&
1150 "damax=",damax,"edriftmax=",edriftmax,&
1154 call MPI_Abort(MPI_COMM_WORLD,IERROR,IERRCODE)
1158 ! First step of the velocity Verlet algorithm
1163 else if (lang.eq.3) then
1165 call sd_verlet1_ciccotti
1167 else if (lang.eq.1) then
1172 ! Build the chain from the newly calculated coordinates
1173 call chainbuild_cart
1174 if (rattle) call rattle1
1176 if (large.and. mod(itime,ntwe).eq.0) then
1177 write (iout,*) "Cartesian and internal coordinates: step 1"
1182 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(dc(j,i),j=1,3),&
1183 (dc(j,i+nres),j=1,3)
1185 write (iout,*) "Accelerations"
1187 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_a(j,i),j=1,3),&
1188 (d_a(j,i+nres),j=1,3)
1190 write (iout,*) "Velocities, step 1"
1192 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),&
1193 (d_t(j,i+nres),j=1,3)
1202 ! Calculate energy and forces
1204 call etotal(potEcomp)
1205 ! AL 4/17/17: Reduce the steps if NaNs occurred.
1206 if (potEcomp(0).gt.0.99e20 .or. isnan(potEcomp(0)).gt.0) then
1211 if (large.and. mod(itime,ntwe).eq.0) &
1212 call enerprint(potEcomp)
1215 t_etotal=t_etotal+MPI_Wtime()-tt0
1217 t_etotal=t_etotal+tcpu()-tt0
1220 potE=potEcomp(0)-potEcomp(20)
1222 ! Get the new accelerations
1225 t_enegrad=t_enegrad+MPI_Wtime()-tt0
1227 t_enegrad=t_enegrad+tcpu()-tt0
1229 ! Determine maximum acceleration and scale down the timestep if needed
1231 amax=amax/(itime_scal+1)**2
1232 call predict_edrift(epdrift)
1233 if (amax/(itime_scal+1).gt.damax .or. epdrift.gt.edriftmax) then
1234 ! Maximum acceleration or maximum predicted energy drift exceeded, rescale the time step
1236 ifac_time=dmax1(dlog(amax/damax),dlog(epdrift/edriftmax)) &
1238 itime_scal=itime_scal+ifac_time
1239 ! fac_time=dmin1(damax/amax,0.5d0)
1240 fac_time=0.5d0**ifac_time
1241 d_time=d_time*fac_time
1242 if (lang.eq.2 .or. lang.eq.3) then
1244 ! write (iout,*) "Calling sd_verlet_setup: 1"
1245 ! Rescale the stochastic forces and recalculate or restore
1246 ! the matrices of tinker integrator
1247 if (itime_scal.gt.maxflag_stoch) then
1248 if (large) write (iout,'(a,i5,a)') &
1249 "Calculate matrices for stochastic step;",&
1250 " itime_scal ",itime_scal
1252 call sd_verlet_p_setup
1254 call sd_verlet_ciccotti_setup
1256 write (iout,'(2a,i3,a,i3,1h.)') &
1257 "Warning: cannot store matrices for stochastic",&
1258 " integration because the index",itime_scal,&
1259 " is greater than",maxflag_stoch
1260 write (iout,'(2a)')"Increase MAXFLAG_STOCH or use direct",&
1261 " integration Langevin algorithm for better efficiency."
1262 else if (flag_stoch(itime_scal)) then
1263 if (large) write (iout,'(a,i5,a,l1)') &
1264 "Restore matrices for stochastic step; itime_scal ",&
1265 itime_scal," flag ",flag_stoch(itime_scal)
1268 pfric_mat(i,j)=pfric0_mat(i,j,itime_scal)
1269 afric_mat(i,j)=afric0_mat(i,j,itime_scal)
1270 vfric_mat(i,j)=vfric0_mat(i,j,itime_scal)
1271 prand_mat(i,j)=prand0_mat(i,j,itime_scal)
1272 vrand_mat1(i,j)=vrand0_mat1(i,j,itime_scal)
1273 vrand_mat2(i,j)=vrand0_mat2(i,j,itime_scal)
1277 if (large) write (iout,'(2a,i5,a,l1)') &
1278 "Calculate & store matrices for stochastic step;",&
1279 " itime_scal ",itime_scal," flag ",flag_stoch(itime_scal)
1281 call sd_verlet_p_setup
1283 call sd_verlet_ciccotti_setup
1285 flag_stoch(ifac_time)=.true.
1288 pfric0_mat(i,j,itime_scal)=pfric_mat(i,j)
1289 afric0_mat(i,j,itime_scal)=afric_mat(i,j)
1290 vfric0_mat(i,j,itime_scal)=vfric_mat(i,j)
1291 prand0_mat(i,j,itime_scal)=prand_mat(i,j)
1292 vrand0_mat1(i,j,itime_scal)=vrand_mat1(i,j)
1293 vrand0_mat2(i,j,itime_scal)=vrand_mat2(i,j)
1297 fac_time=1.0d0/dsqrt(fac_time)
1299 stochforcvec(i)=fac_time*stochforcvec(i)
1302 else if (lang.eq.1) then
1303 ! Rescale the accelerations due to stochastic forces
1304 fac_time=1.0d0/dsqrt(fac_time)
1306 d_as_work(i)=d_as_work(i)*fac_time
1309 if (large) write (iout,'(a,i10,a,f8.6,a,i3,a,i3)') &
1310 "itime",itime," Timestep scaled down to ",&
1311 d_time," ifac_time",ifac_time," itime_scal",itime_scal
1313 ! Second step of the velocity Verlet algorithm
1318 else if (lang.eq.3) then
1320 call sd_verlet2_ciccotti
1322 else if (lang.eq.1) then
1327 if (rattle) call rattle2
1330 if (d_time.ne.d_time0) then
1333 if (lang.eq.2 .or. lang.eq.3) then
1334 if (large) write (iout,'(a)') &
1335 "Restore original matrices for stochastic step"
1336 ! write (iout,*) "Calling sd_verlet_setup: 2"
1337 ! Restore the matrices of tinker integrator if the time step has been restored
1340 pfric_mat(i,j)=pfric0_mat(i,j,0)
1341 afric_mat(i,j)=afric0_mat(i,j,0)
1342 vfric_mat(i,j)=vfric0_mat(i,j,0)
1343 prand_mat(i,j)=prand0_mat(i,j,0)
1344 vrand_mat1(i,j)=vrand0_mat1(i,j,0)
1345 vrand_mat2(i,j)=vrand0_mat2(i,j,0)
1354 ! Calculate the kinetic and the total energy and the kinetic temperature
1358 ! call kinetic1(EK1)
1359 ! write (iout,*) "step",itime," EK",EK," EK1",EK1
1361 ! Couple the system to Berendsen bath if needed
1362 if (tbf .and. lang.eq.0) then
1365 kinetic_T=2.0d0/(dimen3*Rb)*EK
1366 ! Backup the coordinates, velocities, and accelerations
1370 d_t_old(j,i)=d_t(j,i)
1371 d_a_old(j,i)=d_a(j,i)
1375 if (mod(itime,ntwe).eq.0 .and. large) then
1376 write (iout,*) "Velocities, step 2"
1378 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),&
1379 (d_t(j,i+nres),j=1,3)
1384 end subroutine velverlet_step
1385 !-----------------------------------------------------------------------------
1386 subroutine RESPA_step(itime)
1387 !-------------------------------------------------------------------------------
1388 ! Perform a single RESPA step.
1389 !-------------------------------------------------------------------------------
1390 ! implicit real*8 (a-h,o-z)
1391 ! include 'DIMENSIONS'
1395 use control, only:tcpu
1397 ! use io_conf, only:cartprint
1400 integer :: IERROR,ERRCODE
1402 ! include 'COMMON.SETUP'
1403 ! include 'COMMON.CONTROL'
1404 ! include 'COMMON.VAR'
1405 ! include 'COMMON.MD'
1407 ! include 'COMMON.LANGEVIN'
1409 ! include 'COMMON.LANGEVIN.lang0'
1411 ! include 'COMMON.CHAIN'
1412 ! include 'COMMON.DERIV'
1413 ! include 'COMMON.GEO'
1414 ! include 'COMMON.LOCAL'
1415 ! include 'COMMON.INTERACT'
1416 ! include 'COMMON.IOUNITS'
1417 ! include 'COMMON.NAMES'
1418 ! include 'COMMON.TIME1'
1419 real(kind=8),dimension(0:n_ene) :: energia_short,energia_long
1420 real(kind=8),dimension(3) :: L,vcm,incr
1421 real(kind=8),dimension(3,0:2*nres) :: dc_old0,d_t_old0,d_a_old0 !(3,0:maxres2) maxres2=2*maxres
1422 logical :: PRINT_AMTS_MSG = .false.
1423 integer :: count,rstcount !ilen,
1425 character(len=50) :: tytul
1426 integer :: maxcount_scale = 10
1427 !el common /gucio/ cm
1428 !el real(kind=8),dimension(6*nres) :: stochforcvec !(MAXRES6) maxres6=6*maxres
1429 !el common /stochcalc/ stochforcvec
1430 integer :: itime,itt,i,j,itsplit
1432 !el common /cipiszcze/ itt
1434 real(kind=8) :: epdrift,tt0,epdriftmax
1437 if (.not.allocated(stochforcvec)) allocate(stochforcvec(6*nres)) !(MAXRES6) maxres6=6*maxres
1441 if (large.and. mod(itime,ntwe).eq.0) then
1442 write (iout,*) "***************** RESPA itime",itime
1443 write (iout,*) "Cartesian and internal coordinates: step 0"
1445 call pdbout(0.0d0,"cipiszcze",iout)
1447 write (iout,*) "Accelerations from long-range forces"
1449 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_a(j,i),j=1,3),&
1450 (d_a(j,i+nres),j=1,3)
1452 write (iout,*) "Velocities, step 0"
1454 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),&
1455 (d_t(j,i+nres),j=1,3)
1460 ! Perform the initial RESPA step (increment velocities)
1461 ! write (iout,*) "*********************** RESPA ini"
1464 if (mod(itime,ntwe).eq.0 .and. large) then
1465 write (iout,*) "Velocities, end"
1467 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),&
1468 (d_t(j,i+nres),j=1,3)
1472 ! Compute the short-range forces
1478 ! 7/2/2009 commented out
1480 ! call etotal_short(energia_short)
1483 ! 7/2/2009 Copy accelerations due to short-lange forces from previous MD step
1486 d_a(j,i)=d_a_short(j,i)
1490 if (large.and. mod(itime,ntwe).eq.0) then
1491 write (iout,*) "energia_short",energia_short(0)
1492 write (iout,*) "Accelerations from short-range forces"
1494 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_a(j,i),j=1,3),&
1495 (d_a(j,i+nres),j=1,3)
1500 t_enegrad=t_enegrad+MPI_Wtime()-tt0
1502 t_enegrad=t_enegrad+tcpu()-tt0
1507 d_t_old(j,i)=d_t(j,i)
1508 d_a_old(j,i)=d_a(j,i)
1511 ! 6/30/08 A-MTS: attempt at increasing the split number
1514 dc_old0(j,i)=dc_old(j,i)
1515 d_t_old0(j,i)=d_t_old(j,i)
1516 d_a_old0(j,i)=d_a_old(j,i)
1519 if (ntime_split.gt.ntime_split0) ntime_split=ntime_split/2
1520 if (ntime_split.lt.ntime_split0) ntime_split=ntime_split0
1527 ! write (iout,*) "itime",itime," ntime_split",ntime_split
1528 ! Split the time step
1529 d_time=d_time0/ntime_split
1530 ! Perform the short-range RESPA steps (velocity Verlet increments of
1531 ! positions and velocities using short-range forces)
1532 ! write (iout,*) "*********************** RESPA split"
1533 do itsplit=1,ntime_split
1536 else if (lang.eq.2 .or. lang.eq.3) then
1538 call stochastic_force(stochforcvec)
1541 "LANG=2 or 3 NOT SUPPORTED. Recompile without -DLANG0"
1543 call MPI_Abort(MPI_COMM_WORLD,IERROR,ERRCODE)
1548 ! First step of the velocity Verlet algorithm
1553 else if (lang.eq.3) then
1555 call sd_verlet1_ciccotti
1557 else if (lang.eq.1) then
1562 ! Build the chain from the newly calculated coordinates
1563 call chainbuild_cart
1564 if (rattle) call rattle1
1566 if (large.and. mod(itime,ntwe).eq.0) then
1567 write (iout,*) "***** ITSPLIT",itsplit
1568 write (iout,*) "Cartesian and internal coordinates: step 1"
1569 call pdbout(0.0d0,"cipiszcze",iout)
1572 write (iout,*) "Velocities, step 1"
1574 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),&
1575 (d_t(j,i+nres),j=1,3)
1584 ! Calculate energy and forces
1586 call etotal_short(energia_short)
1587 ! AL 4/17/17: Exit itime_split loop when energy goes infinite
1588 if (energia_short(0).gt.0.99e20 .or. isnan(energia_short(0)) ) then
1589 if (PRINT_AMTS_MSG) &
1590 write (iout,*) "Infinities/NaNs in energia_short",energia_short(0),"; increasing ntime_split to",ntime_split
1591 ntime_split=ntime_split*2
1592 if (ntime_split.gt.maxtime_split) then
1595 "Cannot rescue the run; aborting job. Retry with a smaller time step"
1597 call MPI_Abort(MPI_COMM_WORLD,IERROR,ERRCODE)
1600 "Cannot rescue the run; terminating. Retry with a smaller time step"
1606 if (large.and. mod(itime,ntwe).eq.0) &
1607 call enerprint(energia_short)
1610 t_eshort=t_eshort+MPI_Wtime()-tt0
1612 t_eshort=t_eshort+tcpu()-tt0
1616 ! Get the new accelerations
1618 ! 7/2/2009 Copy accelerations due to short-lange forces to an auxiliary array
1621 d_a_short(j,i)=d_a(j,i)
1625 if (large.and. mod(itime,ntwe).eq.0) then
1626 write (iout,*)"energia_short",energia_short(0)
1627 write (iout,*) "Accelerations from short-range forces"
1629 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_a(j,i),j=1,3),&
1630 (d_a(j,i+nres),j=1,3)
1635 ! Determine maximum acceleration and scale down the timestep if needed
1637 amax=amax/ntime_split**2
1638 call predict_edrift(epdrift)
1639 if (ntwe.gt.0 .and. large .and. mod(itime,ntwe).eq.0) &
1640 write (iout,*) "amax",amax," damax",damax,&
1641 " epdrift",epdrift," epdriftmax",epdriftmax
1642 ! Exit loop and try with increased split number if the change of
1643 ! acceleration is too big
1644 if (amax.gt.damax .or. epdrift.gt.edriftmax) then
1645 if (ntime_split.lt.maxtime_split) then
1647 ntime_split=ntime_split*2
1648 ! AL 4/17/17: We should exit the itime_split loop when acceleration change is too big
1652 dc_old(j,i)=dc_old0(j,i)
1653 d_t_old(j,i)=d_t_old0(j,i)
1654 d_a_old(j,i)=d_a_old0(j,i)
1657 if (PRINT_AMTS_MSG) then
1658 write (iout,*) "acceleration/energy drift too large",amax,&
1659 epdrift," split increased to ",ntime_split," itime",itime,&
1665 "Uh-hu. Bumpy landscape. Maximum splitting number",&
1667 " already reached!!! Trying to carry on!"
1671 t_enegrad=t_enegrad+MPI_Wtime()-tt0
1673 t_enegrad=t_enegrad+tcpu()-tt0
1675 ! Second step of the velocity Verlet algorithm
1680 else if (lang.eq.3) then
1682 call sd_verlet2_ciccotti
1684 else if (lang.eq.1) then
1689 if (rattle) call rattle2
1690 ! Backup the coordinates, velocities, and accelerations
1694 d_t_old(j,i)=d_t(j,i)
1695 d_a_old(j,i)=d_a(j,i)
1702 ! Restore the time step
1704 ! Compute long-range forces
1711 call etotal_long(energia_long)
1712 if (energia_long(0).gt.0.99e20 .or. isnan(energia_long(0))) then
1715 "Infinitied/NaNs in energia_long, Aborting MPI job."
1717 call MPI_Abort(MPI_COMM_WORLD,IERROR,ERRCODE)
1719 write (iout,*) "Infinitied/NaNs in energia_long, terminating."
1723 if (large.and. mod(itime,ntwe).eq.0) &
1724 call enerprint(energia_long)
1727 t_elong=t_elong+MPI_Wtime()-tt0
1729 t_elong=t_elong+tcpu()-tt0
1735 t_enegrad=t_enegrad+MPI_Wtime()-tt0
1737 t_enegrad=t_enegrad+tcpu()-tt0
1739 ! Compute accelerations from long-range forces
1741 if (large.and. mod(itime,ntwe).eq.0) then
1742 write (iout,*) "energia_long",energia_long(0)
1743 write (iout,*) "Cartesian and internal coordinates: step 2"
1745 call pdbout(0.0d0,"cipiszcze",iout)
1747 write (iout,*) "Accelerations from long-range forces"
1749 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_a(j,i),j=1,3),&
1750 (d_a(j,i+nres),j=1,3)
1752 write (iout,*) "Velocities, step 2"
1754 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),&
1755 (d_t(j,i+nres),j=1,3)
1759 ! Compute the final RESPA step (increment velocities)
1760 ! write (iout,*) "*********************** RESPA fin"
1762 ! Compute the complete potential energy
1764 potEcomp(i)=energia_short(i)+energia_long(i)
1766 potE=potEcomp(0)-potEcomp(20)
1767 ! potE=energia_short(0)+energia_long(0)
1770 ! Calculate the kinetic and the total energy and the kinetic temperature
1773 ! Couple the system to Berendsen bath if needed
1774 if (tbf .and. lang.eq.0) then
1777 kinetic_T=2.0d0/(dimen3*Rb)*EK
1778 ! Backup the coordinates, velocities, and accelerations
1780 if (mod(itime,ntwe).eq.0 .and. large) then
1781 write (iout,*) "Velocities, end"
1783 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),&
1784 (d_t(j,i+nres),j=1,3)
1789 end subroutine RESPA_step
1790 !-----------------------------------------------------------------------------
1791 subroutine RESPA_vel
1792 ! First and last RESPA step (incrementing velocities using long-range
1795 ! implicit real*8 (a-h,o-z)
1796 ! include 'DIMENSIONS'
1797 ! include 'COMMON.CONTROL'
1798 ! include 'COMMON.VAR'
1799 ! include 'COMMON.MD'
1800 ! include 'COMMON.CHAIN'
1801 ! include 'COMMON.DERIV'
1802 ! include 'COMMON.GEO'
1803 ! include 'COMMON.LOCAL'
1804 ! include 'COMMON.INTERACT'
1805 ! include 'COMMON.IOUNITS'
1806 ! include 'COMMON.NAMES'
1807 integer :: i,j,inres,mnum
1810 d_t(j,0)=d_t(j,0)+0.5d0*d_a(j,0)*d_time
1814 d_t(j,i)=d_t(j,i)+0.5d0*d_a(j,i)*d_time
1819 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
1820 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
1821 .and.(mnum.ne.5)) then
1824 d_t(j,inres)=d_t(j,inres)+0.5d0*d_a(j,inres)*d_time
1829 end subroutine RESPA_vel
1830 !-----------------------------------------------------------------------------
1832 ! Applying velocity Verlet algorithm - step 1 to coordinates
1834 ! implicit real*8 (a-h,o-z)
1835 ! include 'DIMENSIONS'
1836 ! include 'COMMON.CONTROL'
1837 ! include 'COMMON.VAR'
1838 ! include 'COMMON.MD'
1839 ! include 'COMMON.CHAIN'
1840 ! include 'COMMON.DERIV'
1841 ! include 'COMMON.GEO'
1842 ! include 'COMMON.LOCAL'
1843 ! include 'COMMON.INTERACT'
1844 ! include 'COMMON.IOUNITS'
1845 ! include 'COMMON.NAMES'
1846 real(kind=8) :: adt,adt2
1847 integer :: i,j,inres,mnum
1850 write (iout,*) "VELVERLET1 START: DC"
1852 write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3),&
1853 (dc(j,i+nres),j=1,3)
1857 adt=d_a_old(j,0)*d_time
1859 dc(j,0)=dc_old(j,0)+(d_t_old(j,0)+adt2)*d_time
1860 d_t_new(j,0)=d_t_old(j,0)+adt2
1861 d_t(j,0)=d_t_old(j,0)+adt
1865 adt=d_a_old(j,i)*d_time
1867 dc(j,i)=dc_old(j,i)+(d_t_old(j,i)+adt2)*d_time
1868 d_t_new(j,i)=d_t_old(j,i)+adt2
1869 d_t(j,i)=d_t_old(j,i)+adt
1874 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
1875 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
1876 .and.(mnum.ne.5)) then
1879 adt=d_a_old(j,inres)*d_time
1881 dc(j,inres)=dc_old(j,inres)+(d_t_old(j,inres)+adt2)*d_time
1882 d_t_new(j,inres)=d_t_old(j,inres)+adt2
1883 d_t(j,inres)=d_t_old(j,inres)+adt
1888 write (iout,*) "VELVERLET1 END: DC"
1890 write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3),&
1891 (dc(j,i+nres),j=1,3)
1895 end subroutine verlet1
1896 !-----------------------------------------------------------------------------
1898 ! Step 2 of the velocity Verlet algorithm: update velocities
1900 ! implicit real*8 (a-h,o-z)
1901 ! include 'DIMENSIONS'
1902 ! include 'COMMON.CONTROL'
1903 ! include 'COMMON.VAR'
1904 ! include 'COMMON.MD'
1905 ! include 'COMMON.CHAIN'
1906 ! include 'COMMON.DERIV'
1907 ! include 'COMMON.GEO'
1908 ! include 'COMMON.LOCAL'
1909 ! include 'COMMON.INTERACT'
1910 ! include 'COMMON.IOUNITS'
1911 ! include 'COMMON.NAMES'
1912 integer :: i,j,inres,mnum
1915 d_t(j,0)=d_t_new(j,0)+0.5d0*d_a(j,0)*d_time
1919 d_t(j,i)=d_t_new(j,i)+0.5d0*d_a(j,i)*d_time
1924 ! iti=iabs(itype(i,mnum))
1925 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
1926 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
1927 .and.(mnum.ne.5)) then
1930 d_t(j,inres)=d_t_new(j,inres)+0.5d0*d_a(j,inres)*d_time
1935 end subroutine verlet2
1936 !-----------------------------------------------------------------------------
1937 subroutine sddir_precalc
1938 ! Applying velocity Verlet algorithm - step 1 to coordinates
1939 ! implicit real*8 (a-h,o-z)
1940 ! include 'DIMENSIONS'
1946 ! include 'COMMON.CONTROL'
1947 ! include 'COMMON.VAR'
1948 ! include 'COMMON.MD'
1950 ! include 'COMMON.LANGEVIN'
1952 ! include 'COMMON.LANGEVIN.lang0'
1954 ! include 'COMMON.CHAIN'
1955 ! include 'COMMON.DERIV'
1956 ! include 'COMMON.GEO'
1957 ! include 'COMMON.LOCAL'
1958 ! include 'COMMON.INTERACT'
1959 ! include 'COMMON.IOUNITS'
1960 ! include 'COMMON.NAMES'
1961 ! include 'COMMON.TIME1'
1962 !el real(kind=8),dimension(6*nres) :: stochforcvec !(MAXRES6) maxres6=6*maxres
1963 !el common /stochcalc/ stochforcvec
1964 real(kind=8) :: time00
1966 ! Compute friction and stochastic forces
1971 time_fric=time_fric+MPI_Wtime()-time00
1973 call stochastic_force(stochforcvec)
1974 time_stoch=time_stoch+MPI_Wtime()-time00
1977 ! Compute the acceleration due to friction forces (d_af_work) and stochastic
1978 ! forces (d_as_work)
1980 call ginv_mult(fric_work, d_af_work)
1981 call ginv_mult(stochforcvec, d_as_work)
1983 end subroutine sddir_precalc
1984 !-----------------------------------------------------------------------------
1985 subroutine sddir_verlet1
1986 ! Applying velocity Verlet algorithm - step 1 to velocities
1989 ! implicit real*8 (a-h,o-z)
1990 ! include 'DIMENSIONS'
1991 ! include 'COMMON.CONTROL'
1992 ! include 'COMMON.VAR'
1993 ! include 'COMMON.MD'
1995 ! include 'COMMON.LANGEVIN'
1997 ! include 'COMMON.LANGEVIN.lang0'
1999 ! include 'COMMON.CHAIN'
2000 ! include 'COMMON.DERIV'
2001 ! include 'COMMON.GEO'
2002 ! include 'COMMON.LOCAL'
2003 ! include 'COMMON.INTERACT'
2004 ! include 'COMMON.IOUNITS'
2005 ! include 'COMMON.NAMES'
2006 ! Revised 3/31/05 AL: correlation between random contributions to
2007 ! position and velocity increments included.
2008 real(kind=8) :: sqrt13 = 0.57735026918962576451d0 ! 1/sqrt(3)
2009 real(kind=8) :: adt,adt2
2010 integer :: i,j,ind,inres,mnum
2012 ! Add the contribution from BOTH friction and stochastic force to the
2013 ! coordinates, but ONLY the contribution from the friction forces to velocities
2016 adt=(d_a_old(j,0)+d_af_work(j))*d_time
2017 adt2=0.5d0*adt+sqrt13*d_as_work(j)*d_time
2018 dc(j,0)=dc_old(j,0)+(d_t_old(j,0)+adt2)*d_time
2019 d_t_new(j,0)=d_t_old(j,0)+0.5d0*adt
2020 d_t(j,0)=d_t_old(j,0)+adt
2025 adt=(d_a_old(j,i)+d_af_work(ind+j))*d_time
2026 adt2=0.5d0*adt+sqrt13*d_as_work(ind+j)*d_time
2027 dc(j,i)=dc_old(j,i)+(d_t_old(j,i)+adt2)*d_time
2028 d_t_new(j,i)=d_t_old(j,i)+0.5d0*adt
2029 d_t(j,i)=d_t_old(j,i)+adt
2035 ! iti=iabs(itype(i,mnum))
2036 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
2037 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
2038 .and.(mnum.ne.5)) then
2041 adt=(d_a_old(j,inres)+d_af_work(ind+j))*d_time
2042 adt2=0.5d0*adt+sqrt13*d_as_work(ind+j)*d_time
2043 dc(j,inres)=dc_old(j,inres)+(d_t_old(j,inres)+adt2)*d_time
2044 d_t_new(j,inres)=d_t_old(j,inres)+0.5d0*adt
2045 d_t(j,inres)=d_t_old(j,inres)+adt
2051 end subroutine sddir_verlet1
2052 !-----------------------------------------------------------------------------
2053 subroutine sddir_verlet2
2054 ! Calculating the adjusted velocities for accelerations
2057 ! implicit real*8 (a-h,o-z)
2058 ! include 'DIMENSIONS'
2059 ! include 'COMMON.CONTROL'
2060 ! include 'COMMON.VAR'
2061 ! include 'COMMON.MD'
2063 ! include 'COMMON.LANGEVIN'
2065 ! include 'COMMON.LANGEVIN.lang0'
2067 ! include 'COMMON.CHAIN'
2068 ! include 'COMMON.DERIV'
2069 ! include 'COMMON.GEO'
2070 ! include 'COMMON.LOCAL'
2071 ! include 'COMMON.INTERACT'
2072 ! include 'COMMON.IOUNITS'
2073 ! include 'COMMON.NAMES'
2074 real(kind=8),dimension(6*nres) :: stochforcvec,d_as_work1 !(MAXRES6) maxres6=6*maxres
2075 real(kind=8) :: cos60 = 0.5d0, sin60 = 0.86602540378443864676d0
2076 integer :: i,j,ind,inres,mnum
2077 ! Revised 3/31/05 AL: correlation between random contributions to
2078 ! position and velocity increments included.
2079 ! The correlation coefficients are calculated at low-friction limit.
2080 ! Also, friction forces are now not calculated with new velocities.
2082 ! call friction_force
2083 call stochastic_force(stochforcvec)
2085 ! Compute the acceleration due to friction forces (d_af_work) and stochastic
2086 ! forces (d_as_work)
2088 call ginv_mult(stochforcvec, d_as_work1)
2094 d_t(j,0)=d_t_new(j,0)+(0.5d0*(d_a(j,0)+d_af_work(j)) &
2095 +sin60*d_as_work(j)+cos60*d_as_work1(j))*d_time
2100 d_t(j,i)=d_t_new(j,i)+(0.5d0*(d_a(j,i)+d_af_work(ind+j)) &
2101 +sin60*d_as_work(ind+j)+cos60*d_as_work1(ind+j))*d_time
2107 ! iti=iabs(itype(i,mnum))
2108 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
2109 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
2110 .and.(mnum.ne.5)) then
2113 d_t(j,inres)=d_t_new(j,inres)+(0.5d0*(d_a(j,inres) &
2114 +d_af_work(ind+j))+sin60*d_as_work(ind+j) &
2115 +cos60*d_as_work1(ind+j))*d_time
2121 end subroutine sddir_verlet2
2122 !-----------------------------------------------------------------------------
2123 subroutine max_accel
2125 ! Find the maximum difference in the accelerations of the the sites
2126 ! at the beginning and the end of the time step.
2129 ! implicit real*8 (a-h,o-z)
2130 ! include 'DIMENSIONS'
2131 ! include 'COMMON.CONTROL'
2132 ! include 'COMMON.VAR'
2133 ! include 'COMMON.MD'
2134 ! include 'COMMON.CHAIN'
2135 ! include 'COMMON.DERIV'
2136 ! include 'COMMON.GEO'
2137 ! include 'COMMON.LOCAL'
2138 ! include 'COMMON.INTERACT'
2139 ! include 'COMMON.IOUNITS'
2140 real(kind=8),dimension(3) :: aux,accel,accel_old
2141 real(kind=8) :: dacc
2145 ! aux(j)=d_a(j,0)-d_a_old(j,0)
2146 accel_old(j)=d_a_old(j,0)
2153 ! 7/3/08 changed to asymmetric difference
2155 ! accel(j)=aux(j)+0.5d0*(d_a(j,i)-d_a_old(j,i))
2156 accel_old(j)=accel_old(j)+0.5d0*d_a_old(j,i)
2157 accel(j)=accel(j)+0.5d0*d_a(j,i)
2158 ! if (dabs(accel(j)).gt.amax) amax=dabs(accel(j))
2159 if (dabs(accel(j)).gt.dabs(accel_old(j))) then
2160 dacc=dabs(accel(j)-accel_old(j))
2161 ! write (iout,*) i,dacc
2162 if (dacc.gt.amax) amax=dacc
2170 accel_old(j)=d_a_old(j,0)
2175 accel_old(j)=accel_old(j)+d_a_old(j,1)
2176 accel(j)=accel(j)+d_a(j,1)
2181 ! iti=iabs(itype(i,mnum))
2182 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
2183 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
2184 .and.(mnum.ne.5)) then
2186 ! accel(j)=accel(j)+d_a(j,i+nres)-d_a_old(j,i+nres)
2187 accel_old(j)=accel_old(j)+d_a_old(j,i+nres)
2188 accel(j)=accel(j)+d_a(j,i+nres)
2192 ! if (dabs(accel(j)).gt.amax) amax=dabs(accel(j))
2193 if (dabs(accel(j)).gt.dabs(accel_old(j))) then
2194 dacc=dabs(accel(j)-accel_old(j))
2195 ! write (iout,*) "side-chain",i,dacc
2196 if (dacc.gt.amax) amax=dacc
2200 accel_old(j)=accel_old(j)+d_a_old(j,i)
2201 accel(j)=accel(j)+d_a(j,i)
2202 ! aux(j)=aux(j)+d_a(j,i)-d_a_old(j,i)
2206 end subroutine max_accel
2207 !-----------------------------------------------------------------------------
2208 subroutine predict_edrift(epdrift)
2210 ! Predict the drift of the potential energy
2213 use control_data, only: lmuca
2214 ! implicit real*8 (a-h,o-z)
2215 ! include 'DIMENSIONS'
2216 ! include 'COMMON.CONTROL'
2217 ! include 'COMMON.VAR'
2218 ! include 'COMMON.MD'
2219 ! include 'COMMON.CHAIN'
2220 ! include 'COMMON.DERIV'
2221 ! include 'COMMON.GEO'
2222 ! include 'COMMON.LOCAL'
2223 ! include 'COMMON.INTERACT'
2224 ! include 'COMMON.IOUNITS'
2225 ! include 'COMMON.MUCA'
2226 real(kind=8) :: epdrift,epdriftij
2228 ! Drift of the potential energy
2234 epdriftij=dabs((d_a(j,i)-d_a_old(j,i))*gcart(j,i))
2235 if (lmuca) epdriftij=epdriftij*factor
2236 ! write (iout,*) "back",i,j,epdriftij
2237 if (epdriftij.gt.epdrift) epdrift=epdriftij
2241 if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1.and.&
2242 molnum(i).ne.5) then
2245 dabs((d_a(j,i+nres)-d_a_old(j,i+nres))*gxcart(j,i))
2246 if (lmuca) epdriftij=epdriftij*factor
2247 ! write (iout,*) "side",i,j,epdriftij
2248 if (epdriftij.gt.epdrift) epdrift=epdriftij
2252 epdrift=0.5d0*epdrift*d_time*d_time
2253 ! write (iout,*) "epdrift",epdrift
2255 end subroutine predict_edrift
2256 !-----------------------------------------------------------------------------
2257 subroutine verlet_bath
2259 ! Coupling to the thermostat by using the Berendsen algorithm
2262 ! implicit real*8 (a-h,o-z)
2263 ! include 'DIMENSIONS'
2264 ! include 'COMMON.CONTROL'
2265 ! include 'COMMON.VAR'
2266 ! include 'COMMON.MD'
2267 ! include 'COMMON.CHAIN'
2268 ! include 'COMMON.DERIV'
2269 ! include 'COMMON.GEO'
2270 ! include 'COMMON.LOCAL'
2271 ! include 'COMMON.INTERACT'
2272 ! include 'COMMON.IOUNITS'
2273 ! include 'COMMON.NAMES'
2274 real(kind=8) :: T_half,fact
2275 integer :: i,j,inres,mnum
2277 T_half=2.0d0/(dimen3*Rb)*EK
2278 fact=dsqrt(1.0d0+(d_time/tau_bath)*(t_bath/T_half-1.0d0))
2279 ! write(iout,*) "T_half", T_half
2280 ! write(iout,*) "EK", EK
2281 ! write(iout,*) "fact", fact
2283 d_t(j,0)=fact*d_t(j,0)
2287 d_t(j,i)=fact*d_t(j,i)
2292 ! iti=iabs(itype(i,mnum))
2293 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
2294 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
2295 .and.(mnum.ne.5)) then
2298 d_t(j,inres)=fact*d_t(j,inres)
2303 end subroutine verlet_bath
2304 !-----------------------------------------------------------------------------
2306 ! Set up the initial conditions of a MD simulation
2309 use control, only:tcpu
2310 !el use io_basic, only:ilen
2313 use minimm, only:minim_dc,minimize,sc_move
2314 use io_config, only:readrst
2315 use io, only:statout
2316 ! implicit real*8 (a-h,o-z)
2317 ! include 'DIMENSIONS'
2320 character(len=16) :: form
2321 integer :: IERROR,ERRCODE
2323 ! include 'COMMON.SETUP'
2324 ! include 'COMMON.CONTROL'
2325 ! include 'COMMON.VAR'
2326 ! include 'COMMON.MD'
2328 ! include 'COMMON.LANGEVIN'
2330 ! include 'COMMON.LANGEVIN.lang0'
2332 ! include 'COMMON.CHAIN'
2333 ! include 'COMMON.DERIV'
2334 ! include 'COMMON.GEO'
2335 ! include 'COMMON.LOCAL'
2336 ! include 'COMMON.INTERACT'
2337 ! include 'COMMON.IOUNITS'
2338 ! include 'COMMON.NAMES'
2339 ! include 'COMMON.REMD'
2340 real(kind=8),dimension(0:n_ene) :: energia_long,energia_short
2341 real(kind=8),dimension(3) :: vcm,incr,L
2342 real(kind=8) :: xv,sigv,lowb,highb
2343 real(kind=8),dimension(6*nres) :: varia !(maxvar) (maxvar=6*maxres)
2344 character(len=256) :: qstr
2347 character(len=50) :: tytul
2348 logical :: file_exist
2349 !el common /gucio/ cm
2350 integer :: i,j,ipos,iq,iw,nft_sc,iretcode,nfun,itime,ierr,mnum
2351 real(kind=8) :: etot,tt0
2355 ! write(iout,*) "d_time", d_time
2356 ! Compute the standard deviations of stochastic forces for Langevin dynamics
2357 ! if the friction coefficients do not depend on surface area
2358 if (lang.gt.0 .and. .not.surfarea) then
2361 stdforcp(i)=stdfp(mnum)*dsqrt(gamp(mnum))
2365 stdforcsc(i)=stdfsc(iabs(itype(i,mnum)),mnum) &
2366 *dsqrt(gamsc(iabs(itype(i,mnum)),mnum))
2369 ! Open the pdb file for snapshotshots
2372 if (ilen(tmpdir).gt.0) &
2373 call copy_to_tmp(pref_orig(:ilen(pref_orig))//"_MD"// &
2374 liczba(:ilen(liczba))//".pdb")
2376 file=prefix(:ilen(prefix))//"_MD"//liczba(:ilen(liczba)) &
2380 if (ilen(tmpdir).gt.0 .and. (me.eq.king .or. .not.traj1file)) &
2381 call copy_to_tmp(pref_orig(:ilen(pref_orig))//"_MD"// &
2382 liczba(:ilen(liczba))//".x")
2383 cartname=prefix(:ilen(prefix))//"_MD"//liczba(:ilen(liczba)) &
2386 if (ilen(tmpdir).gt.0 .and. (me.eq.king .or. .not.traj1file)) &
2387 call copy_to_tmp(pref_orig(:ilen(pref_orig))//"_MD"// &
2388 liczba(:ilen(liczba))//".cx")
2389 cartname=prefix(:ilen(prefix))//"_MD"//liczba(:ilen(liczba)) &
2395 if (ilen(tmpdir).gt.0) &
2396 call copy_to_tmp(pref_orig(:ilen(pref_orig))//"_MD.pdb")
2397 open(ipdb,file=prefix(:ilen(prefix))//"_MD.pdb")
2399 if (ilen(tmpdir).gt.0) &
2400 call copy_to_tmp(pref_orig(:ilen(pref_orig))//"_MD.cx")
2401 cartname=prefix(:ilen(prefix))//"_MD.cx"
2405 write (qstr,'(256(1h ))')
2408 iq = qinfrag(i,iset)*10
2409 iw = wfrag(i,iset)/100
2411 if(me.eq.king.or..not.out1file) &
2412 write (iout,*) "Frag",qinfrag(i,iset),wfrag(i,iset),iq,iw
2413 write (qstr(ipos:ipos+6),'(2h_f,i1,1h_,i1,1h_,i1)') i,iq,iw
2418 iq = qinpair(i,iset)*10
2419 iw = wpair(i,iset)/100
2421 if(me.eq.king.or..not.out1file) &
2422 write (iout,*) "Pair",i,qinpair(i,iset),wpair(i,iset),iq,iw
2423 write (qstr(ipos:ipos+6),'(2h_p,i1,1h_,i1,1h_,i1)') i,iq,iw
2427 ! pdbname=pdbname(:ilen(pdbname)-4)//qstr(:ipos-1)//'.pdb'
2429 ! cartname=cartname(:ilen(cartname)-2)//qstr(:ipos-1)//'.x'
2431 ! cartname=cartname(:ilen(cartname)-3)//qstr(:ipos-1)//'.cx'
2433 ! statname=statname(:ilen(statname)-5)//qstr(:ipos-1)//'.stat'
2437 if (restart1file) then
2439 inquire(file=mremd_rst_name,exist=file_exist)
2440 write (*,*) me," Before broadcast: file_exist",file_exist
2442 call MPI_Bcast(file_exist,1,MPI_LOGICAL,king,CG_COMM,&
2445 write (*,*) me," After broadcast: file_exist",file_exist
2446 ! inquire(file=mremd_rst_name,exist=file_exist)
2447 if(me.eq.king.or..not.out1file) &
2448 write(iout,*) "Initial state read by master and distributed"
2450 if (ilen(tmpdir).gt.0) &
2451 call copy_to_tmp(pref_orig(:ilen(pref_orig))//'_' &
2452 //liczba(:ilen(liczba))//'.rst')
2453 inquire(file=rest2name,exist=file_exist)
2456 if(.not.restart1file) then
2457 if(me.eq.king.or..not.out1file) &
2458 write(iout,*) "Initial state will be read from file ",&
2459 rest2name(:ilen(rest2name))
2462 call rescale_weights(t_bath)
2464 if(me.eq.king.or..not.out1file)then
2465 if (restart1file) then
2466 write(iout,*) "File ",mremd_rst_name(:ilen(mremd_rst_name)),&
2469 write(iout,*) "File ",rest2name(:ilen(rest2name)),&
2472 write(iout,*) "Initial velocities randomly generated"
2479 ! Generate initial velocities
2480 if(me.eq.king.or..not.out1file) &
2481 write(iout,*) "Initial velocities randomly generated"
2486 ! rest2name = prefix(:ilen(prefix))//'.rst'
2487 if(me.eq.king.or..not.out1file)then
2488 write (iout,*) "Initial velocities"
2490 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),&
2491 (d_t(j,i+nres),j=1,3)
2493 ! Zeroing the total angular momentum of the system
2494 write(iout,*) "Calling the zero-angular momentum subroutine"
2497 ! Getting the potential energy and forces and velocities and accelerations
2499 ! write (iout,*) "velocity of the center of the mass:"
2500 ! write (iout,*) (vcm(j),j=1,3)
2502 d_t(j,0)=d_t(j,0)-vcm(j)
2504 ! Removing the velocity of the center of mass
2506 if(me.eq.king.or..not.out1file)then
2507 write (iout,*) "vcm right after adjustment:"
2508 write (iout,*) (vcm(j),j=1,3)
2512 if(iranconf.ne.0 .or.indpdb.gt.0.and..not.unres_pdb .or.preminim) then
2514 print *, 'Calling OVERLAP_SC'
2515 call overlap_sc(fail)
2518 call sc_move(2,nres-1,10,1d10,nft_sc,etot)
2519 print *,'SC_move',nft_sc,etot
2520 if(me.eq.king.or..not.out1file) &
2521 write(iout,*) 'SC_move',nft_sc,etot
2525 print *, 'Calling MINIM_DC'
2526 call minim_dc(etot,iretcode,nfun)
2528 call geom_to_var(nvar,varia)
2529 print *,'Calling MINIMIZE.'
2530 call minimize(etot,varia,iretcode,nfun)
2531 call var_to_geom(nvar,varia)
2533 if(me.eq.king.or..not.out1file) &
2534 write(iout,*) 'SUMSL return code is',iretcode,' eval ',nfun
2537 call chainbuild_cart
2542 kinetic_T=2.0d0/(dimen3*Rb)*EK
2543 if(me.eq.king.or..not.out1file)then
2553 write(iout,*) "before ETOTAL"
2554 call etotal(potEcomp)
2555 if (large) call enerprint(potEcomp)
2558 t_etotal=t_etotal+MPI_Wtime()-tt0
2560 t_etotal=t_etotal+tcpu()-tt0
2567 if (amax*d_time .gt. dvmax) then
2568 d_time=d_time*dvmax/amax
2569 if(me.eq.king.or..not.out1file) write (iout,*) &
2570 "Time step reduced to",d_time,&
2571 " because of too large initial acceleration."
2573 if(me.eq.king.or..not.out1file)then
2574 write(iout,*) "Potential energy and its components"
2575 call enerprint(potEcomp)
2576 ! write(iout,*) (potEcomp(i),i=0,n_ene)
2578 potE=potEcomp(0)-potEcomp(20)
2581 if (ntwe.ne.0) call statout(itime)
2582 if(me.eq.king.or..not.out1file) &
2583 write (iout,'(/a/3(a25,1pe14.5/))') "Initial:", &
2584 " Kinetic energy",EK," Potential energy",potE, &
2585 " Total energy",totE," Maximum acceleration ", &
2588 write (iout,*) "Initial coordinates"
2590 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(c(j,i),j=1,3),&
2593 write (iout,*) "Initial dC"
2595 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(dc(j,i),j=1,3),&
2596 (dc(j,i+nres),j=1,3)
2598 write (iout,*) "Initial velocities"
2599 write (iout,"(13x,' backbone ',23x,' side chain')")
2601 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),&
2602 (d_t(j,i+nres),j=1,3)
2604 write (iout,*) "Initial accelerations"
2606 ! write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_a(j,i),j=1,3),
2607 write (iout,'(i3,3f15.10,3x,3f15.10)') i,(d_a(j,i),j=1,3),&
2608 (d_a(j,i+nres),j=1,3)
2614 d_t_old(j,i)=d_t(j,i)
2615 d_a_old(j,i)=d_a(j,i)
2617 ! write (iout,*) "dc_old",i,(dc_old(j,i),j=1,3)
2626 call etotal_short(energia_short)
2627 if (large) call enerprint(potEcomp)
2630 t_eshort=t_eshort+MPI_Wtime()-tt0
2632 t_eshort=t_eshort+tcpu()-tt0
2637 if(.not.out1file .and. large) then
2638 write (iout,*) "energia_long",energia_long(0),&
2639 " energia_short",energia_short(0),&
2640 " total",energia_long(0)+energia_short(0)
2641 write (iout,*) "Initial fast-force accelerations"
2643 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_a(j,i),j=1,3),&
2644 (d_a(j,i+nres),j=1,3)
2647 ! 7/2/2009 Copy accelerations due to short-lange forces to an auxiliary array
2650 d_a_short(j,i)=d_a(j,i)
2659 call etotal_long(energia_long)
2660 if (large) call enerprint(potEcomp)
2663 t_elong=t_elong+MPI_Wtime()-tt0
2665 t_elong=t_elong+tcpu()-tt0
2670 if(.not.out1file .and. large) then
2671 write (iout,*) "energia_long",energia_long(0)
2672 write (iout,*) "Initial slow-force accelerations"
2674 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_a(j,i),j=1,3),&
2675 (d_a(j,i+nres),j=1,3)
2679 t_enegrad=t_enegrad+MPI_Wtime()-tt0
2681 t_enegrad=t_enegrad+tcpu()-tt0
2685 end subroutine init_MD
2686 !-----------------------------------------------------------------------------
2687 subroutine random_vel
2689 ! implicit real*8 (a-h,o-z)
2691 use random, only:anorm_distr
2693 ! include 'DIMENSIONS'
2694 ! include 'COMMON.CONTROL'
2695 ! include 'COMMON.VAR'
2696 ! include 'COMMON.MD'
2698 ! include 'COMMON.LANGEVIN'
2700 ! include 'COMMON.LANGEVIN.lang0'
2702 ! include 'COMMON.CHAIN'
2703 ! include 'COMMON.DERIV'
2704 ! include 'COMMON.GEO'
2705 ! include 'COMMON.LOCAL'
2706 ! include 'COMMON.INTERACT'
2707 ! include 'COMMON.IOUNITS'
2708 ! include 'COMMON.NAMES'
2709 ! include 'COMMON.TIME1'
2710 real(kind=8) :: xv,sigv,lowb,highb ,Ek1
2713 real(kind=8) ,allocatable, dimension(:) :: DDU1,DDU2,DL2,DL1,xsolv,DML,rs
2714 real(kind=8) :: sumx
2716 real(kind=8) ,allocatable, dimension(:) :: rsold
2717 real (kind=8),allocatable,dimension(:,:) :: matold
2721 integer :: i,j,ii,k,ind,mark,imark,mnum
2722 ! Generate random velocities from Gaussian distribution of mean 0 and std of KT/m
2723 ! First generate velocities in the eigenspace of the G matrix
2724 ! write (iout,*) "Calling random_vel dimen dimen3",dimen,dimen3
2731 sigv=dsqrt((Rb*t_bath)/geigen(i))
2734 d_t_work_new(ii)=anorm_distr(xv,sigv,lowb,highb)
2736 write (iout,*) "i",i," ii",ii," geigen",geigen(i),&
2737 " d_t_work_new",d_t_work_new(ii)
2748 Ek1=Ek1+0.5d0*geigen(i)*d_t_work_new(ii)**2
2751 write (iout,*) "Ek from eigenvectors",Ek1
2752 write (iout,*) "Kinetic temperatures",2*Ek1/(3*dimen*Rb)
2756 ! Transform velocities to UNRES coordinate space
2757 allocate (DL1(2*nres))
2758 allocate (DDU1(2*nres))
2759 allocate (DL2(2*nres))
2760 allocate (DDU2(2*nres))
2761 allocate (xsolv(2*nres))
2762 allocate (DML(2*nres))
2763 allocate (rs(2*nres))
2765 allocate (rsold(2*nres))
2766 allocate (matold(2*nres,2*nres))
2768 matold(1,1)=DMorig(1)
2769 matold(1,2)=DU1orig(1)
2770 matold(1,3)=DU2orig(1)
2771 write (*,*) DMorig(1),DU1orig(1),DU2orig(1)
2776 matold(i,j)=DMorig(i)
2777 matold(i,j-1)=DU1orig(i-1)
2779 matold(i,j-2)=DU2orig(i-2)
2787 matold(i,j+1)=DU1orig(i)
2793 matold(i,j+2)=DU2orig(i)
2797 matold(dimen,dimen)=DMorig(dimen)
2798 matold(dimen,dimen-1)=DU1orig(dimen-1)
2799 matold(dimen,dimen-2)=DU2orig(dimen-2)
2800 write(iout,*) "old gmatrix"
2801 call matout(dimen,dimen,2*nres,2*nres,matold)
2805 ! Find the ith eigenvector of the pentadiagonal inertiq matrix
2809 DML(j)=DMorig(j)-geigen(i)
2812 DML(j-1)=DMorig(j)-geigen(i)
2817 DDU1(imark-1)=DU2orig(imark-1)
2818 do j=imark+1,dimen-1
2819 DDU1(j-1)=DU1orig(j)
2827 DDU2(j)=DU2orig(j+1)
2836 write (iout,*) "DL2,DL1,DML,DDU1,DDU2"
2837 write(iout,'(10f10.5)') (DL2(k),k=3,dimen-1)
2838 write(iout,'(10f10.5)') (DL1(k),k=2,dimen-1)
2839 write(iout,'(10f10.5)') (DML(k),k=1,dimen-1)
2840 write(iout,'(10f10.5)') (DDU1(k),k=1,dimen-2)
2841 write(iout,'(10f10.5)') (DDU2(k),k=1,dimen-3)
2844 if (imark.gt.2) rs(imark-2)=-DU2orig(imark-2)
2845 if (imark.gt.1) rs(imark-1)=-DU1orig(imark-1)
2846 if (imark.lt.dimen) rs(imark)=-DU1orig(imark)
2847 if (imark.lt.dimen-1) rs(imark+1)=-DU2orig(imark)
2851 ! write (iout,*) "Vector rs"
2853 ! write (iout,*) j,rs(j)
2856 call FDIAG(dimen-1,DL2,DL1,DML,DDU1,DDU2,rs,xsolv,mark)
2863 sumx=-geigen(i)*xsolv(j)
2865 sumx=sumx+matold(j,k)*xsolv(k)
2868 sumx=sumx+matold(j,k)*xsolv(k-1)
2870 write(iout,'(i5,3f10.5)') j,sumx,rsold(j),sumx-rsold(j)
2873 sumx=-geigen(i)*xsolv(j-1)
2875 sumx=sumx+matold(j,k)*xsolv(k)
2878 sumx=sumx+matold(j,k)*xsolv(k-1)
2880 write(iout,'(i5,3f10.5)') j-1,sumx,rsold(j-1),sumx-rsold(j-1)
2884 "Solution of equations system",i," for eigenvalue",geigen(i)
2886 write(iout,'(i5,f10.5)') j,xsolv(j)
2889 do j=dimen-1,imark,-1
2894 write (iout,*) "Un-normalized eigenvector",i," for eigenvalue",geigen(i)
2896 write(iout,'(i5,f10.5)') j,xsolv(j)
2899 ! Normalize ith eigenvector
2902 sumx=sumx+xsolv(j)**2
2906 xsolv(j)=xsolv(j)/sumx
2909 write (iout,*) "Eigenvector",i," for eigenvalue",geigen(i)
2911 write(iout,'(i5,3f10.5)') j,xsolv(j)
2914 ! All done at this point for eigenvector i, exit loop
2922 write (iout,*) "Unable to find eigenvector",i
2925 ! write (iout,*) "i=",i
2927 ! write (iout,*) "k=",k
2930 ! write(iout,*) "ind",ind," ind1",3*(i-1)+k
2931 d_t_work(ind)=d_t_work(ind) &
2932 +xsolv(j)*d_t_work_new(3*(i-1)+k)
2935 enddo ! i (loop over the eigenvectors)
2938 write (iout,*) "d_t_work"
2940 write (iout,"(i5,f10.5)") i,d_t_work(i)
2945 ! if (itype(i,1).eq.10) then
2947 if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
2948 iti=iabs(itype(i,mnum))
2949 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
2950 if (itype(i,1).eq.10 .or. itype(i,mnum).eq.ntyp1_molec(mnum)&
2951 .or.(mnum.eq.5)) then
2958 ! write (iout,*) "k",k," ii+k",ii+k," ii+j+k",ii+j+k,"EK1",Ek1
2959 Ek1=Ek1+0.5d0*mp(mnum)*((d_t_work(ii+j+k)+d_t_work_new(ii+k))/2)**2+&
2960 0.5d0*0.25d0*IP(mnum)*(d_t_work(ii+j+k)-d_t_work_new(ii+k))**2
2963 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
2964 .and.(mnum.ne.5)) ii=ii+3
2965 write (iout,*) "i",i," itype",itype(i,mnum)," mass",msc(itype(i,mnum),mnum)
2966 write (iout,*) "ii",ii
2969 write (iout,*) "k",k," ii",ii,"EK1",EK1
2970 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
2972 Ek1=Ek1+0.5d0*Isc(iabs(itype(i,mnum)),mnum)*(d_t_work(ii)-d_t_work(ii-3))**2
2973 Ek1=Ek1+0.5d0*msc(iabs(itype(i,mnum)),mnum)*d_t_work(ii)**2
2975 write (iout,*) "i",i," ii",ii
2977 write (iout,*) "Ek from d_t_work",Ek1
2978 write (iout,*) "Kinetic temperatures",2*Ek1/(3*dimen*Rb)
2980 if(allocated(DDU1)) deallocate(DDU1)
2981 if(allocated(DDU2)) deallocate(DDU2)
2982 if(allocated(DL2)) deallocate(DL2)
2983 if(allocated(DL1)) deallocate(DL1)
2984 if(allocated(xsolv)) deallocate(xsolv)
2985 if(allocated(DML)) deallocate(DML)
2986 if(allocated(rs)) deallocate(rs)
2988 if(allocated(matold)) deallocate(matold)
2989 if(allocated(rsold)) deallocate(rsold)
2994 d_t(k,j)=d_t_work(ind)
2998 if (itype(j,1).ne.10 .and. itype(j,mnum).ne.ntyp1_molec(mnum)&
2999 .and.(mnum.ne.5)) then
3001 d_t(k,j+nres)=d_t_work(ind)
3007 write (iout,*) "Random velocities in the Calpha,SC space"
3009 write (iout,'(i3,3f10.5)') i,(d_t(j,i),j=1,3)
3012 write (iout,'(i3,3f10.5)') i,(d_t(j,i+nres),j=1,3)
3019 ! if (itype(i,1).eq.10) then
3021 if (itype(i,1).eq.10 .or. itype(i,mnum).eq.ntyp1_molec(mnum)&
3022 .or.(mnum.eq.5)) then
3024 d_t(j,i)=d_t(j,i+1)-d_t(j,i)
3028 d_t(j,i+nres)=d_t(j,i+nres)-d_t(j,i)
3029 d_t(j,i)=d_t(j,i+1)-d_t(j,i)
3034 write (iout,*)"Random velocities in the virtual-bond-vector space"
3036 write (iout,'(i3,3f10.5)') i,(d_t(j,i),j=1,3)
3039 write (iout,'(i3,3f10.5)') i,(d_t(j,i+nres),j=1,3)
3042 write (iout,*) "Ek from d_t_work",Ek1
3043 write (iout,*) "Kinetic temperatures",2*Ek1/(3*dimen*Rb)
3051 d_t_work(ind)=d_t_work(ind) &
3052 +Gvec(i,j)*d_t_work_new((j-1)*3+k+1)
3054 ! write (iout,*) "i",i," ind",ind," d_t_work",d_t_work(ind)
3058 ! Transfer to the d_t vector
3060 d_t(j,0)=d_t_work(j)
3066 d_t(j,i)=d_t_work(ind)
3071 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
3072 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
3073 .and.(mnum.ne.5)) then
3076 d_t(j,i+nres)=d_t_work(ind)
3082 ! write (iout,*) "Kinetic energy",Ek,EK1," kinetic temperature",&
3083 ! 2.0d0/(dimen3*Rb)*EK,2.0d0/(dimen3*Rb)*EK1
3085 ! write(iout,*) "end init MD"
3087 end subroutine random_vel
3088 !-----------------------------------------------------------------------------
3090 subroutine sd_verlet_p_setup
3091 ! Sets up the parameters of stochastic Verlet algorithm
3092 ! implicit real*8 (a-h,o-z)
3093 ! include 'DIMENSIONS'
3094 use control, only: tcpu
3099 ! include 'COMMON.CONTROL'
3100 ! include 'COMMON.VAR'
3101 ! include 'COMMON.MD'
3103 ! include 'COMMON.LANGEVIN'
3105 ! include 'COMMON.LANGEVIN.lang0'
3107 ! include 'COMMON.CHAIN'
3108 ! include 'COMMON.DERIV'
3109 ! include 'COMMON.GEO'
3110 ! include 'COMMON.LOCAL'
3111 ! include 'COMMON.INTERACT'
3112 ! include 'COMMON.IOUNITS'
3113 ! include 'COMMON.NAMES'
3114 ! include 'COMMON.TIME1'
3115 real(kind=8),dimension(6*nres) :: emgdt !(MAXRES6) maxres6=6*maxres
3116 real(kind=8) :: pterm,vterm,rho,rhoc,vsig
3117 real(kind=8),dimension(6*nres) :: pfric_vec,vfric_vec,afric_vec,&
3118 prand_vec,vrand_vec1,vrand_vec2 !(MAXRES6) maxres6=6*maxres
3119 logical :: lprn = .false.
3120 real(kind=8) :: zero = 1.0d-8, gdt_radius = 0.05d0
3121 real(kind=8) :: ktm,gdt,egdt,gdt2,gdt3,gdt4,gdt5,gdt6,gdt7,gdt8,&
3123 integer :: i,maxres2
3130 ! AL 8/17/04 Code adapted from tinker
3132 ! Get the frictional and random terms for stochastic dynamics in the
3133 ! eigenspace of mass-scaled UNRES friction matrix
3137 gdt = fricgam(i) * d_time
3139 ! Stochastic dynamics reduces to simple MD for zero friction
3141 if (gdt .le. zero) then
3142 pfric_vec(i) = 1.0d0
3143 vfric_vec(i) = d_time
3144 afric_vec(i) = 0.5d0 * d_time * d_time
3145 prand_vec(i) = 0.0d0
3146 vrand_vec1(i) = 0.0d0
3147 vrand_vec2(i) = 0.0d0
3149 ! Analytical expressions when friction coefficient is large
3152 if (gdt .ge. gdt_radius) then
3155 vfric_vec(i) = (1.0d0-egdt) / fricgam(i)
3156 afric_vec(i) = (d_time-vfric_vec(i)) / fricgam(i)
3157 pterm = 2.0d0*gdt - 3.0d0 + (4.0d0-egdt)*egdt
3158 vterm = 1.0d0 - egdt**2
3159 rho = (1.0d0-egdt)**2 / sqrt(pterm*vterm)
3161 ! Use series expansions when friction coefficient is small
3172 afric_vec(i) = (gdt2/2.0d0 - gdt3/6.0d0 + gdt4/24.0d0 &
3173 - gdt5/120.0d0 + gdt6/720.0d0 &
3174 - gdt7/5040.0d0 + gdt8/40320.0d0 &
3175 - gdt9/362880.0d0) / fricgam(i)**2
3176 vfric_vec(i) = d_time - fricgam(i)*afric_vec(i)
3177 pfric_vec(i) = 1.0d0 - fricgam(i)*vfric_vec(i)
3178 pterm = 2.0d0*gdt3/3.0d0 - gdt4/2.0d0 &
3179 + 7.0d0*gdt5/30.0d0 - gdt6/12.0d0 &
3180 + 31.0d0*gdt7/1260.0d0 - gdt8/160.0d0 &
3181 + 127.0d0*gdt9/90720.0d0
3182 vterm = 2.0d0*gdt - 2.0d0*gdt2 + 4.0d0*gdt3/3.0d0 &
3183 - 2.0d0*gdt4/3.0d0 + 4.0d0*gdt5/15.0d0 &
3184 - 4.0d0*gdt6/45.0d0 + 8.0d0*gdt7/315.0d0 &
3185 - 2.0d0*gdt8/315.0d0 + 4.0d0*gdt9/2835.0d0
3186 rho = sqrt(3.0d0) * (0.5d0 - 3.0d0*gdt/16.0d0 &
3187 - 17.0d0*gdt2/1280.0d0 &
3188 + 17.0d0*gdt3/6144.0d0 &
3189 + 40967.0d0*gdt4/34406400.0d0 &
3190 - 57203.0d0*gdt5/275251200.0d0 &
3191 - 1429487.0d0*gdt6/13212057600.0d0)
3194 ! Compute the scaling factors of random terms for the nonzero friction case
3196 ktm = 0.5d0*d_time/fricgam(i)
3197 psig = dsqrt(ktm*pterm) / fricgam(i)
3198 vsig = dsqrt(ktm*vterm)
3199 rhoc = dsqrt(1.0d0 - rho*rho)
3201 vrand_vec1(i) = vsig * rho
3202 vrand_vec2(i) = vsig * rhoc
3207 "pfric_vec, vfric_vec, afric_vec, prand_vec, vrand_vec1,",&
3210 write (iout,'(i5,6e15.5)') i,pfric_vec(i),vfric_vec(i),&
3211 afric_vec(i),prand_vec(i),vrand_vec1(i),vrand_vec2(i)
3215 ! Transform from the eigenspace of mass-scaled friction matrix to UNRES variables
3218 call eigtransf(dimen,maxres2,mt3,mt2,pfric_vec,pfric_mat)
3219 call eigtransf(dimen,maxres2,mt3,mt2,vfric_vec,vfric_mat)
3220 call eigtransf(dimen,maxres2,mt3,mt2,afric_vec,afric_mat)
3221 call eigtransf(dimen,maxres2,mt3,mt1,prand_vec,prand_mat)
3222 call eigtransf(dimen,maxres2,mt3,mt1,vrand_vec1,vrand_mat1)
3223 call eigtransf(dimen,maxres2,mt3,mt1,vrand_vec2,vrand_mat2)
3226 t_sdsetup=t_sdsetup+MPI_Wtime()
3228 t_sdsetup=t_sdsetup+tcpu()-tt0
3231 end subroutine sd_verlet_p_setup
3232 !-----------------------------------------------------------------------------
3233 subroutine eigtransf1(n,ndim,ab,d,c)
3237 real(kind=8) :: ab(ndim,ndim,n),c(ndim,n),d(ndim)
3243 c(i,j)=c(i,j)+ab(k,j,i)*d(k)
3248 end subroutine eigtransf1
3249 !-----------------------------------------------------------------------------
3250 subroutine eigtransf(n,ndim,a,b,d,c)
3254 real(kind=8) :: a(ndim,n),b(ndim,n),c(ndim,n),d(ndim)
3260 c(i,j)=c(i,j)+a(i,k)*b(k,j)*d(k)
3265 end subroutine eigtransf
3266 !-----------------------------------------------------------------------------
3267 subroutine sd_verlet1
3269 ! Applying stochastic velocity Verlet algorithm - step 1 to velocities
3271 ! implicit real*8 (a-h,o-z)
3272 ! include 'DIMENSIONS'
3273 ! include 'COMMON.CONTROL'
3274 ! include 'COMMON.VAR'
3275 ! include 'COMMON.MD'
3277 ! include 'COMMON.LANGEVIN'
3279 ! include 'COMMON.LANGEVIN.lang0'
3281 ! include 'COMMON.CHAIN'
3282 ! include 'COMMON.DERIV'
3283 ! include 'COMMON.GEO'
3284 ! include 'COMMON.LOCAL'
3285 ! include 'COMMON.INTERACT'
3286 ! include 'COMMON.IOUNITS'
3287 ! include 'COMMON.NAMES'
3288 !el real(kind=8),dimension(6*nres) :: stochforcvec !(MAXRES6) maxres6=6*maxres
3289 !el common /stochcalc/ stochforcvec
3290 logical :: lprn = .false.
3291 real(kind=8) :: ddt1,ddt2
3292 integer :: i,j,ind,inres
3294 ! write (iout,*) "dc_old"
3296 ! write (iout,'(i5,3f10.5,5x,3f10.5)')
3297 ! & i,(dc_old(j,i),j=1,3),(dc_old(j,i+nres),j=1,3)
3300 dc_work(j)=dc_old(j,0)
3301 d_t_work(j)=d_t_old(j,0)
3302 d_a_work(j)=d_a_old(j,0)
3307 dc_work(ind+j)=dc_old(j,i)
3308 d_t_work(ind+j)=d_t_old(j,i)
3309 d_a_work(ind+j)=d_a_old(j,i)
3315 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
3316 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
3317 .and.(mnum.ne.5)) then
3319 dc_work(ind+j)=dc_old(j,i+nres)
3320 d_t_work(ind+j)=d_t_old(j,i+nres)
3321 d_a_work(ind+j)=d_a_old(j,i+nres)
3329 "pfric_mat, vfric_mat, afric_mat, prand_mat, vrand_mat1,",&
3333 write (iout,'(2i5,6e15.5)') i,j,pfric_mat(i,j),&
3334 vfric_mat(i,j),afric_mat(i,j),&
3335 prand_mat(i,j),vrand_mat1(i,j),vrand_mat2(i,j)
3343 dc_work(i)=dc_work(i)+vfric_mat(i,j)*d_t_work(j) &
3344 +afric_mat(i,j)*d_a_work(j)+prand_mat(i,j)*stochforcvec(j)
3345 ddt1=ddt1+pfric_mat(i,j)*d_t_work(j)
3346 ddt2=ddt2+vfric_mat(i,j)*d_a_work(j)
3348 d_t_work_new(i)=ddt1+0.5d0*ddt2
3349 d_t_work(i)=ddt1+ddt2
3354 d_t(j,0)=d_t_work(j)
3359 dc(j,i)=dc_work(ind+j)
3360 d_t(j,i)=d_t_work(ind+j)
3366 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
3367 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
3368 .and.(mnum.ne.5)) then
3371 dc(j,inres)=dc_work(ind+j)
3372 d_t(j,inres)=d_t_work(ind+j)
3378 end subroutine sd_verlet1
3379 !-----------------------------------------------------------------------------
3380 subroutine sd_verlet2
3382 ! Calculating the adjusted velocities for accelerations
3384 ! implicit real*8 (a-h,o-z)
3385 ! include 'DIMENSIONS'
3386 ! include 'COMMON.CONTROL'
3387 ! include 'COMMON.VAR'
3388 ! include 'COMMON.MD'
3390 ! include 'COMMON.LANGEVIN'
3392 ! include 'COMMON.LANGEVIN.lang0'
3394 ! include 'COMMON.CHAIN'
3395 ! include 'COMMON.DERIV'
3396 ! include 'COMMON.GEO'
3397 ! include 'COMMON.LOCAL'
3398 ! include 'COMMON.INTERACT'
3399 ! include 'COMMON.IOUNITS'
3400 ! include 'COMMON.NAMES'
3401 !el real(kind=8),dimension(6*nres) :: stochforcvec,stochforcvecV !(MAXRES6) maxres6=6*maxres
3402 real(kind=8),dimension(6*nres) :: stochforcvecV !(MAXRES6) maxres6=6*maxres
3403 !el common /stochcalc/ stochforcvec
3405 real(kind=8) :: ddt1,ddt2
3406 integer :: i,j,ind,inres
3407 ! Compute the stochastic forces which contribute to velocity change
3409 call stochastic_force(stochforcvecV)
3416 ddt1=ddt1+vfric_mat(i,j)*d_a_work(j)
3417 ddt2=ddt2+vrand_mat1(i,j)*stochforcvec(j)+ &
3418 vrand_mat2(i,j)*stochforcvecV(j)
3420 d_t_work(i)=d_t_work_new(i)+0.5d0*ddt1+ddt2
3424 d_t(j,0)=d_t_work(j)
3429 d_t(j,i)=d_t_work(ind+j)
3435 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
3436 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
3437 .and.(mnum.ne.5)) then
3440 d_t(j,inres)=d_t_work(ind+j)
3446 end subroutine sd_verlet2
3447 !-----------------------------------------------------------------------------
3448 subroutine sd_verlet_ciccotti_setup
3450 ! Sets up the parameters of stochastic velocity Verlet algorithmi; Ciccotti's
3452 ! implicit real*8 (a-h,o-z)
3453 ! include 'DIMENSIONS'
3454 use control, only: tcpu
3459 ! include 'COMMON.CONTROL'
3460 ! include 'COMMON.VAR'
3461 ! include 'COMMON.MD'
3463 ! include 'COMMON.LANGEVIN'
3465 ! include 'COMMON.LANGEVIN.lang0'
3467 ! include 'COMMON.CHAIN'
3468 ! include 'COMMON.DERIV'
3469 ! include 'COMMON.GEO'
3470 ! include 'COMMON.LOCAL'
3471 ! include 'COMMON.INTERACT'
3472 ! include 'COMMON.IOUNITS'
3473 ! include 'COMMON.NAMES'
3474 ! include 'COMMON.TIME1'
3475 real(kind=8),dimension(6*nres) :: emgdt !(MAXRES6) maxres6=6*maxres
3476 real(kind=8) :: pterm,vterm,rho,rhoc,vsig
3477 real(kind=8),dimension(6*nres) :: pfric_vec,vfric_vec,afric_vec,&
3478 prand_vec,vrand_vec1,vrand_vec2 !(MAXRES6) maxres6=6*maxres
3479 logical :: lprn = .false.
3480 real(kind=8) :: zero = 1.0d-8, gdt_radius = 0.05d0
3481 real(kind=8) :: ktm,gdt,egdt,tt0
3482 integer :: i,maxres2
3489 ! AL 8/17/04 Code adapted from tinker
3491 ! Get the frictional and random terms for stochastic dynamics in the
3492 ! eigenspace of mass-scaled UNRES friction matrix
3496 write (iout,*) "i",i," fricgam",fricgam(i)
3497 gdt = fricgam(i) * d_time
3499 ! Stochastic dynamics reduces to simple MD for zero friction
3501 if (gdt .le. zero) then
3502 pfric_vec(i) = 1.0d0
3503 vfric_vec(i) = d_time
3504 afric_vec(i) = 0.5d0*d_time*d_time
3505 prand_vec(i) = afric_vec(i)
3506 vrand_vec2(i) = vfric_vec(i)
3508 ! Analytical expressions when friction coefficient is large
3513 vfric_vec(i) = dexp(-0.5d0*gdt)*d_time
3514 afric_vec(i) = 0.5d0*dexp(-0.25d0*gdt)*d_time*d_time
3515 prand_vec(i) = afric_vec(i)
3516 vrand_vec2(i) = vfric_vec(i)
3518 ! Compute the scaling factors of random terms for the nonzero friction case
3520 ! ktm = 0.5d0*d_time/fricgam(i)
3521 ! psig = dsqrt(ktm*pterm) / fricgam(i)
3522 ! vsig = dsqrt(ktm*vterm)
3523 ! prand_vec(i) = psig*afric_vec(i)
3524 ! vrand_vec2(i) = vsig*vfric_vec(i)
3529 "pfric_vec, vfric_vec, afric_vec, prand_vec, vrand_vec1,",&
3532 write (iout,'(i5,6e15.5)') i,pfric_vec(i),vfric_vec(i),&
3533 afric_vec(i),prand_vec(i),vrand_vec1(i),vrand_vec2(i)
3537 ! Transform from the eigenspace of mass-scaled friction matrix to UNRES variables
3539 call eigtransf(dimen,maxres2,mt3,mt2,pfric_vec,pfric_mat)
3540 call eigtransf(dimen,maxres2,mt3,mt2,vfric_vec,vfric_mat)
3541 call eigtransf(dimen,maxres2,mt3,mt2,afric_vec,afric_mat)
3542 call eigtransf(dimen,maxres2,mt3,mt1,prand_vec,prand_mat)
3543 call eigtransf(dimen,maxres2,mt3,mt1,vrand_vec2,vrand_mat2)
3545 t_sdsetup=t_sdsetup+MPI_Wtime()
3547 t_sdsetup=t_sdsetup+tcpu()-tt0
3550 end subroutine sd_verlet_ciccotti_setup
3551 !-----------------------------------------------------------------------------
3552 subroutine sd_verlet1_ciccotti
3554 ! Applying stochastic velocity Verlet algorithm - step 1 to velocities
3555 ! implicit real*8 (a-h,o-z)
3557 ! include 'DIMENSIONS'
3561 ! include 'COMMON.CONTROL'
3562 ! include 'COMMON.VAR'
3563 ! include 'COMMON.MD'
3565 ! include 'COMMON.LANGEVIN'
3567 ! include 'COMMON.LANGEVIN.lang0'
3569 ! include 'COMMON.CHAIN'
3570 ! include 'COMMON.DERIV'
3571 ! include 'COMMON.GEO'
3572 ! include 'COMMON.LOCAL'
3573 ! include 'COMMON.INTERACT'
3574 ! include 'COMMON.IOUNITS'
3575 ! include 'COMMON.NAMES'
3576 !el real(kind=8),dimension(6*nres) :: stochforcvec !(MAXRES6) maxres6=6*maxres
3577 !el common /stochcalc/ stochforcvec
3578 logical :: lprn = .false.
3579 real(kind=8) :: ddt1,ddt2
3580 integer :: i,j,ind,inres
3581 ! write (iout,*) "dc_old"
3583 ! write (iout,'(i5,3f10.5,5x,3f10.5)')
3584 ! & i,(dc_old(j,i),j=1,3),(dc_old(j,i+nres),j=1,3)
3587 dc_work(j)=dc_old(j,0)
3588 d_t_work(j)=d_t_old(j,0)
3589 d_a_work(j)=d_a_old(j,0)
3594 dc_work(ind+j)=dc_old(j,i)
3595 d_t_work(ind+j)=d_t_old(j,i)
3596 d_a_work(ind+j)=d_a_old(j,i)
3601 if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
3603 dc_work(ind+j)=dc_old(j,i+nres)
3604 d_t_work(ind+j)=d_t_old(j,i+nres)
3605 d_a_work(ind+j)=d_a_old(j,i+nres)
3614 "pfric_mat, vfric_mat, afric_mat, prand_mat, vrand_mat1,",&
3618 write (iout,'(2i5,6e15.5)') i,j,pfric_mat(i,j),&
3619 vfric_mat(i,j),afric_mat(i,j),&
3620 prand_mat(i,j),vrand_mat1(i,j),vrand_mat2(i,j)
3628 dc_work(i)=dc_work(i)+vfric_mat(i,j)*d_t_work(j) &
3629 +afric_mat(i,j)*d_a_work(j)+prand_mat(i,j)*stochforcvec(j)
3630 ddt1=ddt1+pfric_mat(i,j)*d_t_work(j)
3631 ddt2=ddt2+vfric_mat(i,j)*d_a_work(j)
3633 d_t_work_new(i)=ddt1+0.5d0*ddt2
3634 d_t_work(i)=ddt1+ddt2
3639 d_t(j,0)=d_t_work(j)
3644 dc(j,i)=dc_work(ind+j)
3645 d_t(j,i)=d_t_work(ind+j)
3651 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
3652 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
3653 .and.(mnum.ne.5)) then
3656 dc(j,inres)=dc_work(ind+j)
3657 d_t(j,inres)=d_t_work(ind+j)
3663 end subroutine sd_verlet1_ciccotti
3664 !-----------------------------------------------------------------------------
3665 subroutine sd_verlet2_ciccotti
3667 ! Calculating the adjusted velocities for accelerations
3669 ! implicit real*8 (a-h,o-z)
3670 ! include 'DIMENSIONS'
3671 ! include 'COMMON.CONTROL'
3672 ! include 'COMMON.VAR'
3673 ! include 'COMMON.MD'
3675 ! include 'COMMON.LANGEVIN'
3677 ! include 'COMMON.LANGEVIN.lang0'
3679 ! include 'COMMON.CHAIN'
3680 ! include 'COMMON.DERIV'
3681 ! include 'COMMON.GEO'
3682 ! include 'COMMON.LOCAL'
3683 ! include 'COMMON.INTERACT'
3684 ! include 'COMMON.IOUNITS'
3685 ! include 'COMMON.NAMES'
3686 !el real(kind=8),dimension(6*nres) :: stochforcvec,stochforcvecV !(MAXRES6) maxres6=6*maxres
3687 real(kind=8),dimension(6*nres) :: stochforcvecV !(MAXRES6) maxres6=6*maxres
3688 !el common /stochcalc/ stochforcvec
3689 real(kind=8) :: ddt1,ddt2
3690 integer :: i,j,ind,inres
3692 ! Compute the stochastic forces which contribute to velocity change
3694 call stochastic_force(stochforcvecV)
3701 ddt1=ddt1+vfric_mat(i,j)*d_a_work(j)
3702 ! ddt2=ddt2+vrand_mat2(i,j)*stochforcvecV(j)
3703 ddt2=ddt2+vrand_mat2(i,j)*stochforcvec(j)
3705 d_t_work(i)=d_t_work_new(i)+0.5d0*ddt1+ddt2
3709 d_t(j,0)=d_t_work(j)
3714 d_t(j,i)=d_t_work(ind+j)
3720 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
3722 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
3725 d_t(j,inres)=d_t_work(ind+j)
3731 end subroutine sd_verlet2_ciccotti
3733 !-----------------------------------------------------------------------------
3735 !-----------------------------------------------------------------------------
3736 subroutine inertia_tensor
3738 ! Calculating the intertia tensor for the entire protein in order to
3739 ! remove the perpendicular components of velocity matrix which cause
3740 ! the molecule to rotate.
3743 ! implicit real*8 (a-h,o-z)
3744 ! include 'DIMENSIONS'
3745 ! include 'COMMON.CONTROL'
3746 ! include 'COMMON.VAR'
3747 ! include 'COMMON.MD'
3748 ! include 'COMMON.CHAIN'
3749 ! include 'COMMON.DERIV'
3750 ! include 'COMMON.GEO'
3751 ! include 'COMMON.LOCAL'
3752 ! include 'COMMON.INTERACT'
3753 ! include 'COMMON.IOUNITS'
3754 ! include 'COMMON.NAMES'
3756 real(kind=8),dimension(3,3) :: Im,Imcp,eigvec,Id
3757 real(kind=8),dimension(3) :: pr,eigval,L,vp,vrot
3758 real(kind=8) :: M_SC,mag,mag2,M_PEP
3759 real(kind=8),dimension(3,0:nres) :: vpp !(3,0:MAXRES)
3760 real(kind=8),dimension(3) :: vs_p,pp,incr,v
3761 real(kind=8),dimension(3,3) :: pr1,pr2
3763 !el common /gucio/ cm
3764 integer :: iti,inres,i,j,k,mnum
3775 ! calculating the center of the mass of the protein
3779 if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
3780 if (itype(i,mnum).eq.ntyp1_molec(mnum)) cycle
3781 M_PEP=M_PEP+mp(mnum)
3783 cm(j)=cm(j)+(c(j,i)+0.5d0*dc(j,i))*mp(mnum)
3792 if (mnum.eq.5) cycle
3793 iti=iabs(itype(i,mnum))
3794 M_SC=M_SC+msc(iabs(iti),mnum)
3797 cm(j)=cm(j)+msc(iabs(iti),mnum)*c(j,inres)
3801 cm(j)=cm(j)/(M_SC+M_PEP)
3806 if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
3808 pr(j)=c(j,i)+0.5d0*dc(j,i)-cm(j)
3810 Im(1,1)=Im(1,1)+mp(mnum)*(pr(2)*pr(2)+pr(3)*pr(3))
3811 Im(1,2)=Im(1,2)-mp(mnum)*pr(1)*pr(2)
3812 Im(1,3)=Im(1,3)-mp(mnum)*pr(1)*pr(3)
3813 Im(2,3)=Im(2,3)-mp(mnum)*pr(2)*pr(3)
3814 Im(2,2)=Im(2,2)+mp(mnum)*(pr(3)*pr(3)+pr(1)*pr(1))
3815 Im(3,3)=Im(3,3)+mp(mnum)*(pr(1)*pr(1)+pr(2)*pr(2))
3820 iti=iabs(itype(i,mnum))
3821 if (mnum.eq.5) cycle
3824 pr(j)=c(j,inres)-cm(j)
3826 Im(1,1)=Im(1,1)+msc(iabs(iti),mnum)*(pr(2)*pr(2)+pr(3)*pr(3))
3827 Im(1,2)=Im(1,2)-msc(iabs(iti),mnum)*pr(1)*pr(2)
3828 Im(1,3)=Im(1,3)-msc(iabs(iti),mnum)*pr(1)*pr(3)
3829 Im(2,3)=Im(2,3)-msc(iabs(iti),mnum)*pr(2)*pr(3)
3830 Im(2,2)=Im(2,2)+msc(iabs(iti),mnum)*(pr(3)*pr(3)+pr(1)*pr(1))
3831 Im(3,3)=Im(3,3)+msc(iabs(iti),mnum)*(pr(1)*pr(1)+pr(2)*pr(2))
3836 Im(1,1)=Im(1,1)+Ip(mnum)*(1-dc_norm(1,i)*dc_norm(1,i))* &
3837 vbld(i+1)*vbld(i+1)*0.25d0
3838 Im(1,2)=Im(1,2)+Ip(mnum)*(-dc_norm(1,i)*dc_norm(2,i))* &
3839 vbld(i+1)*vbld(i+1)*0.25d0
3840 Im(1,3)=Im(1,3)+Ip(mnum)*(-dc_norm(1,i)*dc_norm(3,i))* &
3841 vbld(i+1)*vbld(i+1)*0.25d0
3842 Im(2,3)=Im(2,3)+Ip(mnum)*(-dc_norm(2,i)*dc_norm(3,i))* &
3843 vbld(i+1)*vbld(i+1)*0.25d0
3844 Im(2,2)=Im(2,2)+Ip(mnum)*(1-dc_norm(2,i)*dc_norm(2,i))* &
3845 vbld(i+1)*vbld(i+1)*0.25d0
3846 Im(3,3)=Im(3,3)+Ip(mnum)*(1-dc_norm(3,i)*dc_norm(3,i))* &
3847 vbld(i+1)*vbld(i+1)*0.25d0
3853 ! if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)) then
3854 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
3855 .and.(mnum.ne.5)) then
3856 iti=iabs(itype(i,mnum))
3858 Im(1,1)=Im(1,1)+Isc(iti,mnum)*(1-dc_norm(1,inres)* &
3859 dc_norm(1,inres))*vbld(inres)*vbld(inres)
3860 Im(1,2)=Im(1,2)-Isc(iti,mnum)*(dc_norm(1,inres)* &
3861 dc_norm(2,inres))*vbld(inres)*vbld(inres)
3862 Im(1,3)=Im(1,3)-Isc(iti,mnum)*(dc_norm(1,inres)* &
3863 dc_norm(3,inres))*vbld(inres)*vbld(inres)
3864 Im(2,3)=Im(2,3)-Isc(iti,mnum)*(dc_norm(2,inres)* &
3865 dc_norm(3,inres))*vbld(inres)*vbld(inres)
3866 Im(2,2)=Im(2,2)+Isc(iti,mnum)*(1-dc_norm(2,inres)* &
3867 dc_norm(2,inres))*vbld(inres)*vbld(inres)
3868 Im(3,3)=Im(3,3)+Isc(iti,mnum)*(1-dc_norm(3,inres)* &
3869 dc_norm(3,inres))*vbld(inres)*vbld(inres)
3874 ! write(iout,*) "The angular momentum before adjustment:"
3875 ! write(iout,*) (L(j),j=1,3)
3881 ! Copying the Im matrix for the djacob subroutine
3889 ! Finding the eigenvectors and eignvalues of the inertia tensor
3890 call djacob(3,3,10000,1.0d-10,Imcp,eigvec,eigval)
3891 ! write (iout,*) "Eigenvalues & Eigenvectors"
3892 ! write (iout,'(5x,3f10.5)') (eigval(i),i=1,3)
3895 ! write (iout,'(i5,3f10.5)') i,(eigvec(i,j),j=1,3)
3897 ! Constructing the diagonalized matrix
3899 if (dabs(eigval(i)).gt.1.0d-15) then
3900 Id(i,i)=1.0d0/eigval(i)
3907 Imcp(i,j)=eigvec(j,i)
3913 pr1(i,j)=pr1(i,j)+Id(i,k)*Imcp(k,j)
3920 pr2(i,j)=pr2(i,j)+eigvec(i,k)*pr1(k,j)
3924 ! Calculating the total rotational velocity of the molecule
3927 vrot(i)=vrot(i)+pr2(i,j)*L(j)
3930 ! Resetting the velocities
3932 call vecpr(vrot(1),dc(1,i),vp)
3934 d_t(j,i)=d_t(j,i)-vp(j)
3939 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
3940 .and.(mnum.ne.5)) then
3941 ! if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)) then
3942 ! if(itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
3944 call vecpr(vrot(1),dc(1,inres),vp)
3946 d_t(j,inres)=d_t(j,inres)-vp(j)
3951 ! write(iout,*) "The angular momentum after adjustment:"
3952 ! write(iout,*) (L(j),j=1,3)
3955 end subroutine inertia_tensor
3956 !-----------------------------------------------------------------------------
3957 subroutine angmom(cm,L)
3960 ! implicit real*8 (a-h,o-z)
3961 ! include 'DIMENSIONS'
3962 ! include 'COMMON.CONTROL'
3963 ! include 'COMMON.VAR'
3964 ! include 'COMMON.MD'
3965 ! include 'COMMON.CHAIN'
3966 ! include 'COMMON.DERIV'
3967 ! include 'COMMON.GEO'
3968 ! include 'COMMON.LOCAL'
3969 ! include 'COMMON.INTERACT'
3970 ! include 'COMMON.IOUNITS'
3971 ! include 'COMMON.NAMES'
3972 real(kind=8) :: mscab
3973 real(kind=8),dimension(3) :: L,cm,pr,vp,vrot,incr,v,pp
3974 integer :: iti,inres,i,j,mnum
3975 ! Calculate the angular momentum
3984 if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
3986 pr(j)=c(j,i)+0.5d0*dc(j,i)-cm(j)
3989 v(j)=incr(j)+0.5d0*d_t(j,i)
3992 incr(j)=incr(j)+d_t(j,i)
3994 call vecpr(pr(1),v(1),vp)
3996 L(j)=L(j)+mp(mnum)*vp(j)
4000 pp(j)=0.5d0*d_t(j,i)
4002 call vecpr(pr(1),pp(1),vp)
4004 L(j)=L(j)+Ip(mnum)*vp(j)
4012 iti=iabs(itype(i,mnum))
4020 pr(j)=c(j,inres)-cm(j)
4022 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4023 .and.(mnum.ne.5)) then
4025 v(j)=incr(j)+d_t(j,inres)
4032 call vecpr(pr(1),v(1),vp)
4033 ! write (iout,*) "i",i," iti",iti," pr",(pr(j),j=1,3),&
4034 ! " v",(v(j),j=1,3)," vp",(vp(j),j=1,3)
4036 L(j)=L(j)+mscab*vp(j)
4038 ! write (iout,*) "L",(l(j),j=1,3)
4039 if (itype(i,mnum).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4040 .and.(mnum.ne.5)) then
4042 v(j)=incr(j)+d_t(j,inres)
4044 call vecpr(dc(1,inres),d_t(1,inres),vp)
4046 L(j)=L(j)+Isc(iti,mnum)*vp(j)
4050 incr(j)=incr(j)+d_t(j,i)
4054 end subroutine angmom
4055 !-----------------------------------------------------------------------------
4056 subroutine vcm_vel(vcm)
4059 ! implicit real*8 (a-h,o-z)
4060 ! include 'DIMENSIONS'
4061 ! include 'COMMON.VAR'
4062 ! include 'COMMON.MD'
4063 ! include 'COMMON.CHAIN'
4064 ! include 'COMMON.DERIV'
4065 ! include 'COMMON.GEO'
4066 ! include 'COMMON.LOCAL'
4067 ! include 'COMMON.INTERACT'
4068 ! include 'COMMON.IOUNITS'
4069 real(kind=8),dimension(3) :: vcm,vv
4070 real(kind=8) :: summas,amas
4080 if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
4082 summas=summas+mp(mnum)
4084 vcm(j)=vcm(j)+mp(mnum)*(vv(j)+0.5d0*d_t(j,i))
4088 amas=msc(iabs(itype(i,mnum)),mnum)
4093 if (itype(i,mnum).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4094 .and.(mnum.ne.5)) then
4096 vcm(j)=vcm(j)+amas*(vv(j)+d_t(j,i+nres))
4100 vcm(j)=vcm(j)+amas*vv(j)
4104 vv(j)=vv(j)+d_t(j,i)
4107 ! write (iout,*) "vcm",(vcm(j),j=1,3)," summas",summas
4109 vcm(j)=vcm(j)/summas
4112 end subroutine vcm_vel
4113 !-----------------------------------------------------------------------------
4115 !-----------------------------------------------------------------------------
4117 ! RATTLE algorithm for velocity Verlet - step 1, UNRES
4121 ! implicit real*8 (a-h,o-z)
4122 ! include 'DIMENSIONS'
4124 ! include 'COMMON.CONTROL'
4125 ! include 'COMMON.VAR'
4126 ! include 'COMMON.MD'
4128 ! include 'COMMON.LANGEVIN'
4130 ! include 'COMMON.LANGEVIN.lang0'
4132 ! include 'COMMON.CHAIN'
4133 ! include 'COMMON.DERIV'
4134 ! include 'COMMON.GEO'
4135 ! include 'COMMON.LOCAL'
4136 ! include 'COMMON.INTERACT'
4137 ! include 'COMMON.IOUNITS'
4138 ! include 'COMMON.NAMES'
4139 ! include 'COMMON.TIME1'
4140 !el real(kind=8) :: gginv(2*nres,2*nres),&
4141 !el gdc(3,2*nres,2*nres)
4142 real(kind=8) :: dC_uncor(3,2*nres) !,&
4143 !el real(kind=8) :: Cmat(2*nres,2*nres)
4144 real(kind=8) :: x(2*nres),xcorr(3,2*nres) !maxres2=2*maxres
4145 !el common /przechowalnia/ GGinv,gdc,Cmat,nbond
4146 !el common /przechowalnia/ nbond
4147 integer :: max_rattle = 5
4148 logical :: lprn = .false., lprn1 = .false., not_done
4149 real(kind=8) :: tol_rattle = 1.0d-5
4151 integer :: ii,i,j,jj,l,ind,ind1,nres2
4154 !el /common/ przechowalnia
4156 if(.not.allocated(GGinv)) allocate(GGinv(nres2,nres2))
4157 if(.not.allocated(gdc)) allocate(gdc(3,nres2,nres2))
4158 if(.not.allocated(Cmat)) allocate(Cmat(nres2,nres2))
4160 if (lprn) write (iout,*) "RATTLE1"
4164 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4165 .and.(mnum.ne.5)) nbond=nbond+1
4167 ! Make a folded form of the Ginv-matrix
4180 if (j.eq.1 .and. l.eq.1) GGinv(ii,jj)=Ginv(ind,ind1)
4185 if (itype(k,1).ne.10 .and. itype(k,mnum).ne.ntyp1_molec(mnum)&
4186 .and.(mnum.ne.5)) then
4190 if (j.eq.1 .and. l.eq.1) GGinv(ii,jj)=Ginv(ind,ind1)
4198 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4209 if (j.eq.1 .and. l.eq.1) GGinv(ii,jj)=Ginv(ind,ind1)
4213 if (itype(k,1).ne.10) then
4217 if (j.eq.1 .and. l.eq.1) GGinv(ii,jj)=Ginv(ind,ind1)
4225 write (iout,*) "Matrix GGinv"
4226 call MATOUT(nbond,nbond,MAXRES2,MAXRES2,GGinv)
4232 if (iter.gt.max_rattle) then
4233 write (iout,*) "Error - too many iterations in RATTLE."
4236 ! Calculate the matrix C = GG**(-1) dC_old o dC
4241 dC_uncor(j,ind1)=dC(j,i)
4245 if (itype(i,1).ne.10) then
4248 dC_uncor(j,ind1)=dC(j,i+nres)
4257 gdc(j,i,ind)=GGinv(i,ind)*dC_old(j,k)
4261 if (itype(k,1).ne.10) then
4264 gdc(j,i,ind)=GGinv(i,ind)*dC_old(j,k+nres)
4269 ! Calculate deviations from standard virtual-bond lengths
4273 x(ind)=vbld(i+1)**2-vbl**2
4276 if (itype(i,1).ne.10) then
4278 x(ind)=vbld(i+nres)**2-vbldsc0(1,itype(i,1))**2
4282 write (iout,*) "Coordinates and violations"
4284 write(iout,'(i5,3f10.5,5x,e15.5)') &
4285 i,(dC_uncor(j,i),j=1,3),x(i)
4287 write (iout,*) "Velocities and violations"
4291 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4292 i,ind,(d_t_new(j,i),j=1,3),scalar(d_t_new(1,i),dC_old(1,i))
4296 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4297 .and.(mnum.ne.5)) then
4300 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4301 i+nres,ind,(d_t_new(j,i+nres),j=1,3),&
4302 scalar(d_t_new(1,i+nres),dC_old(1,i+nres))
4305 ! write (iout,*) "gdc"
4307 ! write (iout,*) "i",i
4309 ! write (iout,'(i5,3f10.5)') j,(gdc(k,j,i),k=1,3)
4315 if (dabs(x(i)).gt.xmax) then
4319 if (xmax.lt.tol_rattle) then
4323 ! Calculate the matrix of the system of equations
4328 Cmat(i,j)=Cmat(i,j)+dC_uncor(k,i)*gdc(k,i,j)
4333 write (iout,*) "Matrix Cmat"
4334 call MATOUT(nbond,nbond,MAXRES2,MAXRES2,Cmat)
4336 call gauss(Cmat,X,MAXRES2,nbond,1,*10)
4337 ! Add constraint term to positions
4344 xx = xx+x(ii)*gdc(j,ind,ii)
4348 d_t_new(j,i)=d_t_new(j,i)-xx/d_time
4352 if (itype(i,1).ne.10) then
4357 xx = xx+x(ii)*gdc(j,ind,ii)
4360 dC(j,i+nres)=dC(j,i+nres)-xx
4361 d_t_new(j,i+nres)=d_t_new(j,i+nres)-xx/d_time
4365 ! Rebuild the chain using the new coordinates
4366 call chainbuild_cart
4368 write (iout,*) "New coordinates, Lagrange multipliers,",&
4369 " and differences between actual and standard bond lengths"
4373 xx=vbld(i+1)**2-vbl**2
4374 write (iout,'(i5,3f10.5,5x,f10.5,e15.5)') &
4375 i,(dC(j,i),j=1,3),x(ind),xx
4379 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4382 xx=vbld(i+nres)**2-vbldsc0(1,itype(i,1))**2
4383 write (iout,'(i5,3f10.5,5x,f10.5,e15.5)') &
4384 i,(dC(j,i+nres),j=1,3),x(ind),xx
4387 write (iout,*) "Velocities and violations"
4391 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4392 i,ind,(d_t_new(j,i),j=1,3),scalar(d_t_new(1,i),dC_old(1,i))
4395 if (itype(i,1).ne.10) then
4397 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4398 i+nres,ind,(d_t_new(j,i+nres),j=1,3),&
4399 scalar(d_t_new(1,i+nres),dC_old(1,i+nres))
4406 10 write (iout,*) "Error - singularity in solving the system",&
4407 " of equations for Lagrange multipliers."
4411 "RATTLE inactive; use -DRATTLE switch at compile time."
4414 end subroutine rattle1
4415 !-----------------------------------------------------------------------------
4417 ! RATTLE algorithm for velocity Verlet - step 2, UNRES
4421 ! implicit real*8 (a-h,o-z)
4422 ! include 'DIMENSIONS'
4424 ! include 'COMMON.CONTROL'
4425 ! include 'COMMON.VAR'
4426 ! include 'COMMON.MD'
4428 ! include 'COMMON.LANGEVIN'
4430 ! include 'COMMON.LANGEVIN.lang0'
4432 ! include 'COMMON.CHAIN'
4433 ! include 'COMMON.DERIV'
4434 ! include 'COMMON.GEO'
4435 ! include 'COMMON.LOCAL'
4436 ! include 'COMMON.INTERACT'
4437 ! include 'COMMON.IOUNITS'
4438 ! include 'COMMON.NAMES'
4439 ! include 'COMMON.TIME1'
4440 !el real(kind=8) :: gginv(2*nres,2*nres),&
4441 !el gdc(3,2*nres,2*nres)
4442 real(kind=8) :: dC_uncor(3,2*nres) !,&
4443 !el Cmat(2*nres,2*nres)
4444 real(kind=8) :: x(2*nres) !maxres2=2*maxres
4445 !el common /przechowalnia/ GGinv,gdc,Cmat,nbond
4446 !el common /przechowalnia/ nbond
4447 integer :: max_rattle = 5
4448 logical :: lprn = .false., lprn1 = .false., not_done
4449 real(kind=8) :: tol_rattle = 1.0d-5
4453 !el /common/ przechowalnia
4454 if(.not.allocated(GGinv)) allocate(GGinv(nres2,nres2))
4455 if(.not.allocated(gdc)) allocate(gdc(3,nres2,nres2))
4456 if(.not.allocated(Cmat)) allocate(Cmat(nres2,nres2))
4458 if (lprn) write (iout,*) "RATTLE2"
4459 if (lprn) write (iout,*) "Velocity correction"
4460 ! Calculate the matrix G dC
4466 gdc(j,i,ind)=GGinv(i,ind)*dC(j,k)
4471 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4472 .and.(mnum.ne.5)) then
4475 gdc(j,i,ind)=GGinv(i,ind)*dC(j,k+nres)
4481 ! write (iout,*) "gdc"
4483 ! write (iout,*) "i",i
4485 ! write (iout,'(i5,3f10.5)') j,(gdc(k,j,i),k=1,3)
4489 ! Calculate the matrix of the system of equations
4496 Cmat(ind,j)=Cmat(ind,j)+dC(k,i)*gdc(k,ind,j)
4502 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4503 .and.(mnum.ne.5)) then
4508 Cmat(ind,j)=Cmat(ind,j)+dC(k,i+nres)*gdc(k,ind,j)
4513 ! Calculate the scalar product dC o d_t_new
4517 x(ind)=scalar(d_t(1,i),dC(1,i))
4521 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4522 .and.(mnum.ne.5)) then
4524 x(ind)=scalar(d_t(1,i+nres),dC(1,i+nres))
4528 write (iout,*) "Velocities and violations"
4532 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4533 i,ind,(d_t(j,i),j=1,3),x(ind)
4537 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4538 .and.(mnum.ne.5)) then
4540 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4541 i+nres,ind,(d_t(j,i+nres),j=1,3),x(ind)
4547 if (dabs(x(i)).gt.xmax) then
4551 if (xmax.lt.tol_rattle) then
4556 write (iout,*) "Matrix Cmat"
4557 call MATOUT(nbond,nbond,MAXRES2,MAXRES2,Cmat)
4559 call gauss(Cmat,X,MAXRES2,nbond,1,*10)
4560 ! Add constraint term to velocities
4567 xx = xx+x(ii)*gdc(j,ind,ii)
4569 d_t(j,i)=d_t(j,i)-xx
4574 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4575 .and.(mnum.ne.5)) then
4580 xx = xx+x(ii)*gdc(j,ind,ii)
4582 d_t(j,i+nres)=d_t(j,i+nres)-xx
4588 "New velocities, Lagrange multipliers violations"
4592 if (lprn) write (iout,'(2i5,3f10.5,5x,2e15.5)') &
4593 i,ind,(d_t(j,i),j=1,3),x(ind),scalar(d_t(1,i),dC(1,i))
4597 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4600 write (iout,'(2i5,3f10.5,5x,2e15.5)') &
4601 i+nres,ind,(d_t(j,i+nres),j=1,3),x(ind),&
4602 scalar(d_t(1,i+nres),dC(1,i+nres))
4608 10 write (iout,*) "Error - singularity in solving the system",&
4609 " of equations for Lagrange multipliers."
4613 "RATTLE inactive; use -DRATTLE option at compile time."
4616 end subroutine rattle2
4617 !-----------------------------------------------------------------------------
4618 subroutine rattle_brown
4619 ! RATTLE/LINCS algorithm for Brownian dynamics, UNRES
4623 ! implicit real*8 (a-h,o-z)
4624 ! include 'DIMENSIONS'
4626 ! include 'COMMON.CONTROL'
4627 ! include 'COMMON.VAR'
4628 ! include 'COMMON.MD'
4630 ! include 'COMMON.LANGEVIN'
4632 ! include 'COMMON.LANGEVIN.lang0'
4634 ! include 'COMMON.CHAIN'
4635 ! include 'COMMON.DERIV'
4636 ! include 'COMMON.GEO'
4637 ! include 'COMMON.LOCAL'
4638 ! include 'COMMON.INTERACT'
4639 ! include 'COMMON.IOUNITS'
4640 ! include 'COMMON.NAMES'
4641 ! include 'COMMON.TIME1'
4642 !el real(kind=8) :: gginv(2*nres,2*nres),&
4643 !el gdc(3,2*nres,2*nres)
4644 real(kind=8) :: dC_uncor(3,2*nres) !,&
4645 !el real(kind=8) :: Cmat(2*nres,2*nres)
4646 real(kind=8) :: x(2*nres) !maxres2=2*maxres
4647 !el common /przechowalnia/ GGinv,gdc,Cmat,nbond
4648 !el common /przechowalnia/ nbond
4649 integer :: max_rattle = 5
4650 logical :: lprn = .false., lprn1 = .false., not_done
4651 real(kind=8) :: tol_rattle = 1.0d-5
4655 !el /common/ przechowalnia
4656 if(.not.allocated(GGinv)) allocate(GGinv(nres2,nres2))
4657 if(.not.allocated(gdc)) allocate(gdc(3,nres2,nres2))
4658 if(.not.allocated(Cmat)) allocate(Cmat(nres2,nres2))
4661 if (lprn) write (iout,*) "RATTLE_BROWN"
4664 if (itype(i,1).ne.10) nbond=nbond+1
4666 ! Make a folded form of the Ginv-matrix
4679 if (j.eq.1 .and. l.eq.1) GGinv(ii,jj)=fricmat(ind,ind1)
4683 if (itype(k,1).ne.10) then
4687 if (j.eq.1 .and. l.eq.1) GGinv(ii,jj)=fricmat(ind,ind1)
4694 if (itype(i,1).ne.10) then
4704 if (j.eq.1 .and. l.eq.1) GGinv(ii,jj)=fricmat(ind,ind1)
4708 if (itype(k,1).ne.10) then
4712 if (j.eq.1 .and. l.eq.1)GGinv(ii,jj)=fricmat(ind,ind1)
4720 write (iout,*) "Matrix GGinv"
4721 call MATOUT(nbond,nbond,MAXRES2,MAXRES2,GGinv)
4727 if (iter.gt.max_rattle) then
4728 write (iout,*) "Error - too many iterations in RATTLE."
4731 ! Calculate the matrix C = GG**(-1) dC_old o dC
4736 dC_uncor(j,ind1)=dC(j,i)
4740 if (itype(i,1).ne.10) then
4743 dC_uncor(j,ind1)=dC(j,i+nres)
4752 gdc(j,i,ind)=GGinv(i,ind)*dC_old(j,k)
4756 if (itype(k,1).ne.10) then
4759 gdc(j,i,ind)=GGinv(i,ind)*dC_old(j,k+nres)
4764 ! Calculate deviations from standard virtual-bond lengths
4768 x(ind)=vbld(i+1)**2-vbl**2
4771 if (itype(i,1).ne.10) then
4773 x(ind)=vbld(i+nres)**2-vbldsc0(1,itype(i,1))**2
4777 write (iout,*) "Coordinates and violations"
4779 write(iout,'(i5,3f10.5,5x,e15.5)') &
4780 i,(dC_uncor(j,i),j=1,3),x(i)
4782 write (iout,*) "Velocities and violations"
4786 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4787 i,ind,(d_t(j,i),j=1,3),scalar(d_t(1,i),dC_old(1,i))
4790 if (itype(i,1).ne.10) then
4792 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4793 i+nres,ind,(d_t(j,i+nres),j=1,3),&
4794 scalar(d_t(1,i+nres),dC_old(1,i+nres))
4797 write (iout,*) "gdc"
4799 write (iout,*) "i",i
4801 write (iout,'(i5,3f10.5)') j,(gdc(k,j,i),k=1,3)
4807 if (dabs(x(i)).gt.xmax) then
4811 if (xmax.lt.tol_rattle) then
4815 ! Calculate the matrix of the system of equations
4820 Cmat(i,j)=Cmat(i,j)+dC_uncor(k,i)*gdc(k,i,j)
4825 write (iout,*) "Matrix Cmat"
4826 call MATOUT(nbond,nbond,MAXRES2,MAXRES2,Cmat)
4828 call gauss(Cmat,X,MAXRES2,nbond,1,*10)
4829 ! Add constraint term to positions
4836 xx = xx+x(ii)*gdc(j,ind,ii)
4839 d_t(j,i)=d_t(j,i)+xx/d_time
4844 if (itype(i,1).ne.10) then
4849 xx = xx+x(ii)*gdc(j,ind,ii)
4852 d_t(j,i+nres)=d_t(j,i+nres)+xx/d_time
4853 dC(j,i+nres)=dC(j,i+nres)+xx
4857 ! Rebuild the chain using the new coordinates
4858 call chainbuild_cart
4860 write (iout,*) "New coordinates, Lagrange multipliers,",&
4861 " and differences between actual and standard bond lengths"
4865 xx=vbld(i+1)**2-vbl**2
4866 write (iout,'(i5,3f10.5,5x,f10.5,e15.5)') &
4867 i,(dC(j,i),j=1,3),x(ind),xx
4870 if (itype(i,1).ne.10) then
4872 xx=vbld(i+nres)**2-vbldsc0(1,itype(i,1))**2
4873 write (iout,'(i5,3f10.5,5x,f10.5,e15.5)') &
4874 i,(dC(j,i+nres),j=1,3),x(ind),xx
4877 write (iout,*) "Velocities and violations"
4881 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4882 i,ind,(d_t_new(j,i),j=1,3),scalar(d_t_new(1,i),dC_old(1,i))
4885 if (itype(i,1).ne.10) then
4887 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4888 i+nres,ind,(d_t_new(j,i+nres),j=1,3),&
4889 scalar(d_t_new(1,i+nres),dC_old(1,i+nres))
4896 10 write (iout,*) "Error - singularity in solving the system",&
4897 " of equations for Lagrange multipliers."
4901 "RATTLE inactive; use -DRATTLE option at compile time"
4904 end subroutine rattle_brown
4905 !-----------------------------------------------------------------------------
4907 !-----------------------------------------------------------------------------
4908 subroutine friction_force
4913 ! implicit real*8 (a-h,o-z)
4914 ! include 'DIMENSIONS'
4915 ! include 'COMMON.VAR'
4916 ! include 'COMMON.CHAIN'
4917 ! include 'COMMON.DERIV'
4918 ! include 'COMMON.GEO'
4919 ! include 'COMMON.LOCAL'
4920 ! include 'COMMON.INTERACT'
4921 ! include 'COMMON.MD'
4923 ! include 'COMMON.LANGEVIN'
4925 ! include 'COMMON.LANGEVIN.lang0'
4927 ! include 'COMMON.IOUNITS'
4928 !el real(kind=8),dimension(6*nres) :: gamvec !(MAXRES6) maxres6=6*maxres
4929 !el common /syfek/ gamvec
4930 real(kind=8) :: vv(3),vvtot(3,nres),v_work(6*nres) !,&
4931 !el ginvfric(2*nres,2*nres) !maxres2=2*maxres
4932 !el common /przechowalnia/ ginvfric
4934 logical :: lprn = .false., checkmode = .false.
4935 integer :: i,j,ind,k,nres2,nres6,mnum
4939 if(.not.allocated(gamvec)) allocate(gamvec(nres6)) !(MAXRES6)
4940 if(.not.allocated(ginvfric)) allocate(ginvfric(nres2,nres2)) !maxres2=2*maxres
4948 d_t_work(j)=d_t(j,0)
4953 d_t_work(ind+j)=d_t(j,i)
4959 if ((itype(i,1).ne.10).and.(itype(i,mnum).ne.ntyp1_molec(mnum))&
4960 .and.(mnum.ne.5)) then
4962 d_t_work(ind+j)=d_t(j,i+nres)
4968 call fricmat_mult(d_t_work,fric_work)
4970 if (.not.checkmode) return
4973 write (iout,*) "d_t_work and fric_work"
4975 write (iout,'(i3,2e15.5)') i,d_t_work(i),fric_work(i)
4979 friction(j,0)=fric_work(j)
4984 friction(j,i)=fric_work(ind+j)
4990 if ((itype(i,1).ne.10).and.(itype(i,mnum).ne.ntyp1_molec(mnum))&
4991 .and.(mnum.ne.5)) then
4992 ! if ((itype(i,1).ne.10).and.(itype(i,1).ne.ntyp1)) then
4994 friction(j,i+nres)=fric_work(ind+j)
5000 write(iout,*) "Friction backbone"
5002 write(iout,'(i5,3e15.5,5x,3e15.5)') &
5003 i,(friction(j,i),j=1,3),(d_t(j,i),j=1,3)
5005 write(iout,*) "Friction side chain"
5007 write(iout,'(i5,3e15.5,5x,3e15.5)') &
5008 i,(friction(j,i+nres),j=1,3),(d_t(j,i+nres),j=1,3)
5017 vvtot(j,i)=vv(j)+0.5d0*d_t(j,i)
5018 vvtot(j,i+nres)=vv(j)+d_t(j,i+nres)
5019 vv(j)=vv(j)+d_t(j,i)
5022 write (iout,*) "vvtot backbone and sidechain"
5024 write (iout,'(i5,3e15.5,5x,3e15.5)') i,(vvtot(j,i),j=1,3),&
5025 (vvtot(j,i+nres),j=1,3)
5030 v_work(ind+j)=vvtot(j,i)
5036 v_work(ind+j)=vvtot(j,i+nres)
5040 write (iout,*) "v_work gamvec and site-based friction forces"
5042 write (iout,'(i5,3e15.5)') i,v_work(i),gamvec(i),&
5046 ! fric_work1(i)=0.0d0
5048 ! fric_work1(i)=fric_work1(i)-A(j,i)*gamvec(j)*v_work(j)
5051 ! write (iout,*) "fric_work and fric_work1"
5053 ! write (iout,'(i5,2e15.5)') i,fric_work(i),fric_work1(i)
5059 ginvfric(i,j)=ginvfric(i,j)+ginv(i,k)*fricmat(k,j)
5063 write (iout,*) "ginvfric"
5065 write (iout,'(i5,100f8.3)') i,(ginvfric(i,j),j=1,dimen)
5067 write (iout,*) "symmetry check"
5070 write (iout,*) i,j,ginvfric(i,j)-ginvfric(j,i)
5075 end subroutine friction_force
5076 !-----------------------------------------------------------------------------
5077 subroutine setup_fricmat
5081 use control_data, only:time_Bcast
5082 use control, only:tcpu
5084 ! implicit real*8 (a-h,o-z)
5088 real(kind=8) :: time00
5090 ! include 'DIMENSIONS'
5091 ! include 'COMMON.VAR'
5092 ! include 'COMMON.CHAIN'
5093 ! include 'COMMON.DERIV'
5094 ! include 'COMMON.GEO'
5095 ! include 'COMMON.LOCAL'
5096 ! include 'COMMON.INTERACT'
5097 ! include 'COMMON.MD'
5098 ! include 'COMMON.SETUP'
5099 ! include 'COMMON.TIME1'
5100 ! integer licznik /0/
5103 ! include 'COMMON.LANGEVIN'
5105 ! include 'COMMON.LANGEVIN.lang0'
5107 ! include 'COMMON.IOUNITS'
5109 integer :: i,j,ind,ind1,m
5110 logical :: lprn = .false.
5111 real(kind=8) :: dtdi !el ,gamvec(2*nres)
5112 !el real(kind=8),dimension(2*nres,2*nres) :: ginvfric,fcopy
5113 ! real(kind=8),allocatable,dimension(:,:) :: fcopy
5114 !el real(kind=8),dimension(2*nres*(2*nres+1)/2) :: Ghalf !(mmaxres2) (mmaxres2=(maxres2*(maxres2+1)/2))
5115 !el common /syfek/ gamvec
5116 real(kind=8) :: work(8*2*nres)
5117 integer :: iwork(2*nres)
5118 !el common /przechowalnia/ ginvfric,Ghalf,fcopy
5119 integer :: ii,iti,k,l,nzero,nres2,nres6,ierr,mnum
5123 if(.not.allocated(fricmat)) allocate(fricmat(nres2,nres2))
5124 if(.not.allocated(fcopy)) allocate(fcopy(nres2,nres2)) !maxres2=2*maxres
5125 if (fg_rank.ne.king) goto 10
5130 if(.not.allocated(gamvec)) allocate(gamvec(nres2)) !(MAXRES2)
5131 if(.not.allocated(ginvfric)) allocate(ginvfric(nres2,nres2)) !maxres2=2*maxres
5132 if(.not.allocated(fcopy)) allocate(fcopy(nres2,nres2)) !maxres2=2*maxres
5133 !el allocate(fcopy(nres2,nres2)) !maxres2=2*maxres
5134 if(.not.allocated(Ghalf)) allocate(Ghalf(nres2*(nres2+1)/2)) !maxres2=2*maxres
5136 if(.not.allocated(fricmat)) allocate(fricmat(nres2,nres2))
5137 ! Zeroing out fricmat
5143 ! Load the friction coefficients corresponding to peptide groups
5148 gamvec(ind1)=gamp(mnum)
5150 ! Load the friction coefficients corresponding to side chains
5154 gamsc(ntyp1_molec(j),j)=1.0d0
5161 gamvec(ii)=gamsc(iabs(iti),mnum)
5163 if (surfarea) call sdarea(gamvec)
5165 ! write (iout,*) "Matrix A and vector gamma"
5167 ! write (iout,'(i2,$)') i
5169 ! write (iout,'(f4.1,$)') A(i,j)
5171 ! write (iout,'(f8.3)') gamvec(i)
5175 write (iout,*) "Vector gamvec"
5177 write (iout,'(i5,f10.5)') i, gamvec(i)
5181 ! The friction matrix
5186 dtdi=dtdi+A(j,k)*A(j,i)*gamvec(j)
5193 write (iout,'(//a)') "Matrix fricmat"
5194 call matout2(dimen,dimen,nres2,nres2,fricmat)
5196 if (lang.eq.2 .or. lang.eq.3) then
5197 ! Mass-scale the friction matrix if non-direct integration will be performed
5203 Ginvfric(i,j)=Ginvfric(i,j)+ &
5204 Gsqrm(i,k)*Gsqrm(l,j)*fricmat(k,l)
5209 ! Diagonalize the friction matrix
5214 Ghalf(ind)=Ginvfric(i,j)
5217 call gldiag(nres2,dimen,dimen,Ghalf,work,fricgam,fricvec,&
5220 write (iout,'(//2a)') "Eigenvectors and eigenvalues of the",&
5221 " mass-scaled friction matrix"
5222 call eigout(dimen,dimen,nres2,nres2,fricvec,fricgam)
5224 ! Precompute matrices for tinker stochastic integrator
5231 mt1(i,j)=mt1(i,j)+fricvec(k,i)*gsqrm(k,j)
5232 mt2(i,j)=mt2(i,j)+fricvec(k,i)*gsqrp(k,j)
5238 else if (lang.eq.4) then
5239 ! Diagonalize the friction matrix
5244 Ghalf(ind)=fricmat(i,j)
5247 call gldiag(nres2,dimen,dimen,Ghalf,work,fricgam,fricvec,&
5250 write (iout,'(//2a)') "Eigenvectors and eigenvalues of the",&
5252 call eigout(dimen,dimen,nres2,nres2,fricvec,fricgam)
5254 ! Determine the number of zero eigenvalues of the friction matrix
5255 nzero=max0(dimen-dimen1,0)
5256 ! do while (fricgam(nzero+1).le.1.0d-5 .and. nzero.lt.dimen)
5259 write (iout,*) "Number of zero eigenvalues:",nzero
5264 fricmat(i,j)=fricmat(i,j) &
5265 +fricvec(i,k)*fricvec(j,k)/fricgam(k)
5270 write (iout,'(//a)') "Generalized inverse of fricmat"
5271 call matout(dimen,dimen,nres6,nres6,fricmat)
5276 if (nfgtasks.gt.1) then
5277 if (fg_rank.eq.0) then
5278 ! The matching BROADCAST for fg processors is called in ERGASTULUM
5284 call MPI_Bcast(10,1,MPI_INTEGER,king,FG_COMM,IERROR)
5286 time_Bcast=time_Bcast+MPI_Wtime()-time00
5288 time_Bcast=time_Bcast+tcpu()-time00
5290 ! print *,"Processor",myrank,
5291 ! & " BROADCAST iorder in SETUP_FRICMAT"
5294 write (iout,*) "setup_fricmat licznik"!,licznik !sp
5300 ! Scatter the friction matrix
5301 call MPI_Scatterv(fricmat(1,1),nginv_counts(0),&
5302 nginv_start(0),MPI_DOUBLE_PRECISION,fcopy(1,1),&
5303 myginv_ng_count,MPI_DOUBLE_PRECISION,king,FG_COMM,IERROR)
5306 time_scatter=time_scatter+MPI_Wtime()-time00
5307 time_scatter_fmat=time_scatter_fmat+MPI_Wtime()-time00
5309 time_scatter=time_scatter+tcpu()-time00
5310 time_scatter_fmat=time_scatter_fmat+tcpu()-time00
5314 do j=1,2*my_ng_count
5315 fricmat(j,i)=fcopy(i,j)
5318 ! write (iout,*) "My chunk of fricmat"
5319 ! call MATOUT2(my_ng_count,dimen,maxres2,maxres2,fcopy)
5323 end subroutine setup_fricmat
5324 !-----------------------------------------------------------------------------
5325 subroutine stochastic_force(stochforcvec)
5328 use random, only:anorm_distr
5329 ! implicit real*8 (a-h,o-z)
5330 ! include 'DIMENSIONS'
5331 use control, only: tcpu
5336 ! include 'COMMON.VAR'
5337 ! include 'COMMON.CHAIN'
5338 ! include 'COMMON.DERIV'
5339 ! include 'COMMON.GEO'
5340 ! include 'COMMON.LOCAL'
5341 ! include 'COMMON.INTERACT'
5342 ! include 'COMMON.MD'
5343 ! include 'COMMON.TIME1'
5345 ! include 'COMMON.LANGEVIN'
5347 ! include 'COMMON.LANGEVIN.lang0'
5349 ! include 'COMMON.IOUNITS'
5351 real(kind=8) :: x,sig,lowb,highb
5352 real(kind=8) :: ff(3),force(3,0:2*nres),zeta2,lowb2
5353 real(kind=8) :: highb2,sig2,forcvec(6*nres),stochforcvec(6*nres)
5354 real(kind=8) :: time00
5355 logical :: lprn = .false.
5356 integer :: i,j,ind,mnum
5360 stochforc(j,i)=0.0d0
5370 ! Compute the stochastic forces acting on bodies. Store in force.
5376 force(j,i)=anorm_distr(x,sig,lowb,highb)
5384 force(j,i+nres)=anorm_distr(x,sig2,lowb2,highb2)
5388 time_fsample=time_fsample+MPI_Wtime()-time00
5390 time_fsample=time_fsample+tcpu()-time00
5392 ! Compute the stochastic forces acting on virtual-bond vectors.
5398 stochforc(j,i)=ff(j)+0.5d0*force(j,i)
5401 ff(j)=ff(j)+force(j,i)
5403 ! if (itype(i+1,1).ne.ntyp1) then
5405 if (itype(i+1,mnum).ne.ntyp1_molec(mnum)) then
5407 stochforc(j,i)=stochforc(j,i)+force(j,i+nres+1)
5408 ff(j)=ff(j)+force(j,i+nres+1)
5413 stochforc(j,0)=ff(j)+force(j,nnt+nres)
5417 if ((itype(i,1).ne.10).and.(itype(i,mnum).ne.ntyp1_molec(mnum))&
5418 .and.(mnum.ne.5)) then
5419 ! if ((itype(i,1).ne.10).and.(itype(i,1).ne.ntyp1)) then
5421 stochforc(j,i+nres)=force(j,i+nres)
5427 stochforcvec(j)=stochforc(j,0)
5432 stochforcvec(ind+j)=stochforc(j,i)
5438 if ((itype(i,1).ne.10).and.(itype(i,mnum).ne.ntyp1_molec(mnum))&
5439 .and.(mnum.ne.5)) then
5440 ! if ((itype(i,1).ne.10).and.(itype(i,1).ne.ntyp1)) then
5442 stochforcvec(ind+j)=stochforc(j,i+nres)
5448 write (iout,*) "stochforcvec"
5450 write(iout,'(i5,e15.5)') i,stochforcvec(i)
5452 write(iout,*) "Stochastic forces backbone"
5454 write(iout,'(i5,3e15.5)') i,(stochforc(j,i),j=1,3)
5456 write(iout,*) "Stochastic forces side chain"
5458 write(iout,'(i5,3e15.5)') &
5459 i,(stochforc(j,i+nres),j=1,3)
5467 write (iout,*) i,ind
5469 forcvec(ind+j)=force(j,i)
5474 write (iout,*) i,ind
5476 forcvec(j+ind)=force(j,i+nres)
5481 write (iout,*) "forcvec"
5485 write (iout,'(2i3,2f10.5)') i,j,force(j,i),&
5492 write (iout,'(2i3,2f10.5)') i,j,force(j,i+nres),&
5501 end subroutine stochastic_force
5502 !-----------------------------------------------------------------------------
5503 subroutine sdarea(gamvec)
5505 ! Scale the friction coefficients according to solvent accessible surface areas
5506 ! Code adapted from TINKER
5510 ! implicit real*8 (a-h,o-z)
5511 ! include 'DIMENSIONS'
5512 ! include 'COMMON.CONTROL'
5513 ! include 'COMMON.VAR'
5514 ! include 'COMMON.MD'
5516 ! include 'COMMON.LANGEVIN'
5518 ! include 'COMMON.LANGEVIN.lang0'
5520 ! include 'COMMON.CHAIN'
5521 ! include 'COMMON.DERIV'
5522 ! include 'COMMON.GEO'
5523 ! include 'COMMON.LOCAL'
5524 ! include 'COMMON.INTERACT'
5525 ! include 'COMMON.IOUNITS'
5526 ! include 'COMMON.NAMES'
5527 real(kind=8),dimension(2*nres) :: radius,gamvec !(maxres2)
5528 real(kind=8),parameter :: twosix = 1.122462048309372981d0
5529 logical :: lprn = .false.
5530 real(kind=8) :: probe,area,ratio
5531 integer :: i,j,ind,iti,mnum
5533 ! determine new friction coefficients every few SD steps
5535 ! set the atomic radii to estimates of sigma values
5537 ! print *,"Entered sdarea"
5543 ! Load peptide group radii
5546 radius(i)=pstok(mnum)
5548 ! Load side chain radii
5552 radius(i+nres)=restok(iti,mnum)
5555 ! write (iout,*) "i",i," radius",radius(i)
5558 radius(i) = radius(i) / twosix
5559 if (radius(i) .ne. 0.0d0) radius(i) = radius(i) + probe
5562 ! scale atomic friction coefficients by accessible area
5564 if (lprn) write (iout,*) &
5565 "Original gammas, surface areas, scaling factors, new gammas, ",&
5566 "std's of stochastic forces"
5569 if (radius(i).gt.0.0d0) then
5570 call surfatom (i,area,radius)
5571 ratio = dmax1(area/(4.0d0*pi*radius(i)**2),1.0d-1)
5572 if (lprn) write (iout,'(i5,3f10.5,$)') &
5573 i,gamvec(ind+1),area,ratio
5576 gamvec(ind) = ratio * gamvec(ind)
5579 stdforcp(i)=stdfp(mnum)*dsqrt(gamvec(ind))
5580 if (lprn) write (iout,'(2f10.5)') gamvec(ind),stdforcp(i)
5584 if (radius(i+nres).gt.0.0d0) then
5585 call surfatom (i+nres,area,radius)
5586 ratio = dmax1(area/(4.0d0*pi*radius(i+nres)**2),1.0d-1)
5587 if (lprn) write (iout,'(i5,3f10.5,$)') &
5588 i,gamvec(ind+1),area,ratio
5591 gamvec(ind) = ratio * gamvec(ind)
5594 stdforcsc(i)=stdfsc(itype(i,mnum),mnum)*dsqrt(gamvec(ind))
5595 if (lprn) write (iout,'(2f10.5)') gamvec(ind),stdforcsc(i)
5600 end subroutine sdarea
5601 !-----------------------------------------------------------------------------
5603 !-----------------------------------------------------------------------------
5606 ! ###################################################
5607 ! ## COPYRIGHT (C) 1996 by Jay William Ponder ##
5608 ! ## All Rights Reserved ##
5609 ! ###################################################
5611 ! ################################################################
5613 ! ## subroutine surfatom -- exposed surface area of an atom ##
5615 ! ################################################################
5618 ! "surfatom" performs an analytical computation of the surface
5619 ! area of a specified atom; a simplified version of "surface"
5621 ! literature references:
5623 ! T. J. Richmond, "Solvent Accessible Surface Area and
5624 ! Excluded Volume in Proteins", Journal of Molecular Biology,
5627 ! L. Wesson and D. Eisenberg, "Atomic Solvation Parameters
5628 ! Applied to Molecular Dynamics of Proteins in Solution",
5629 ! Protein Science, 1, 227-235 (1992)
5631 ! variables and parameters:
5633 ! ir number of atom for which area is desired
5634 ! area accessible surface area of the atom
5635 ! radius radii of each of the individual atoms
5638 subroutine surfatom(ir,area,radius)
5640 ! implicit real*8 (a-h,o-z)
5641 ! include 'DIMENSIONS'
5643 ! include 'COMMON.GEO'
5644 ! include 'COMMON.IOUNITS'
5646 integer :: nsup,nstart_sup
5647 ! double precision c,dc,dc_old,d_c_work,xloc,xrot,dc_norm
5648 ! common /chain/ c(3,maxres2+2),dc(3,0:maxres2),dc_old(3,0:maxres2),
5649 ! & xloc(3,maxres),xrot(3,maxres),dc_norm(3,0:maxres2),
5650 ! & dc_work(MAXRES6),nres,nres0
5651 integer,parameter :: maxarc=300
5655 integer :: mi,ni,narc
5656 integer :: key(maxarc)
5657 integer :: intag(maxarc)
5658 integer :: intag1(maxarc)
5659 real(kind=8) :: area,arcsum
5660 real(kind=8) :: arclen,exang
5661 real(kind=8) :: delta,delta2
5662 real(kind=8) :: eps,rmove
5663 real(kind=8) :: xr,yr,zr
5664 real(kind=8) :: rr,rrsq
5665 real(kind=8) :: rplus,rminus
5666 real(kind=8) :: axx,axy,axz
5667 real(kind=8) :: ayx,ayy
5668 real(kind=8) :: azx,azy,azz
5669 real(kind=8) :: uxj,uyj,uzj
5670 real(kind=8) :: tx,ty,tz
5671 real(kind=8) :: txb,tyb,td
5672 real(kind=8) :: tr2,tr,txr,tyr
5673 real(kind=8) :: tk1,tk2
5674 real(kind=8) :: thec,the,t,tb
5675 real(kind=8) :: txk,tyk,tzk
5676 real(kind=8) :: t1,ti,tf,tt
5677 real(kind=8) :: txj,tyj,tzj
5678 real(kind=8) :: ccsq,cc,xysq
5679 real(kind=8) :: bsqk,bk,cosine
5680 real(kind=8) :: dsqj,gi,pix2
5681 real(kind=8) :: therk,dk,gk
5682 real(kind=8) :: risqk,rik
5683 real(kind=8) :: radius(2*nres) !(maxatm) (maxatm=maxres2)
5684 real(kind=8) :: ri(maxarc),risq(maxarc)
5685 real(kind=8) :: ux(maxarc),uy(maxarc),uz(maxarc)
5686 real(kind=8) :: xc(maxarc),yc(maxarc),zc(maxarc)
5687 real(kind=8) :: xc1(maxarc),yc1(maxarc),zc1(maxarc)
5688 real(kind=8) :: dsq(maxarc),bsq(maxarc)
5689 real(kind=8) :: dsq1(maxarc),bsq1(maxarc)
5690 real(kind=8) :: arci(maxarc),arcf(maxarc)
5691 real(kind=8) :: ex(maxarc),lt(maxarc),gr(maxarc)
5692 real(kind=8) :: b(maxarc),b1(maxarc),bg(maxarc)
5693 real(kind=8) :: kent(maxarc),kout(maxarc)
5694 real(kind=8) :: ther(maxarc)
5695 logical :: moved,top
5696 logical :: omit(maxarc)
5699 ! maxatm = 2*nres !maxres2 maxres2=2*maxres
5700 ! maxlight = 8*maxatm
5703 ! maxtors = 4*maxatm
5705 ! zero out the surface area for the sphere of interest
5708 ! write (2,*) "ir",ir," radius",radius(ir)
5709 if (radius(ir) .eq. 0.0d0) return
5711 ! set the overlap significance and connectivity shift
5715 delta2 = delta * delta
5720 ! store coordinates and radius of the sphere of interest
5728 ! initialize values of some counters and summations
5737 ! test each sphere to see if it overlaps the sphere of interest
5740 if (i.eq.ir .or. radius(i).eq.0.0d0) goto 30
5741 rplus = rr + radius(i)
5743 if (abs(tx) .ge. rplus) goto 30
5745 if (abs(ty) .ge. rplus) goto 30
5747 if (abs(tz) .ge. rplus) goto 30
5749 ! check for sphere overlap by testing distance against radii
5751 xysq = tx*tx + ty*ty
5752 if (xysq .lt. delta2) then
5759 if (rplus-cc .le. delta) goto 30
5760 rminus = rr - radius(i)
5762 ! check to see if sphere of interest is completely buried
5764 if (cc-abs(rminus) .le. delta) then
5765 if (rminus .le. 0.0d0) goto 170
5769 ! check for too many overlaps with sphere of interest
5771 if (io .ge. maxarc) then
5773 20 format (/,' SURFATOM -- Increase the Value of MAXARC')
5777 ! get overlap between current sphere and sphere of interest
5786 gr(io) = (ccsq+rplus*rminus) / (2.0d0*rr*b1(io))
5792 ! case where no other spheres overlap the sphere of interest
5795 area = 4.0d0 * pi * rrsq
5799 ! case where only one sphere overlaps the sphere of interest
5802 area = pix2 * (1.0d0 + gr(1))
5803 area = mod(area,4.0d0*pi) * rrsq
5807 ! case where many spheres intersect the sphere of interest;
5808 ! sort the intersecting spheres by their degree of overlap
5810 call sort2 (io,gr,key)
5813 intag(i) = intag1(k)
5822 ! get radius of each overlap circle on surface of the sphere
5827 risq(i) = rrsq - gi*gi
5828 ri(i) = sqrt(risq(i))
5829 ther(i) = 0.5d0*pi - asin(min(1.0d0,max(-1.0d0,gr(i))))
5832 ! find boundary of inaccessible area on sphere of interest
5835 if (.not. omit(k)) then
5842 ! check to see if J circle is intersecting K circle;
5843 ! get distance between circle centers and sum of radii
5846 if (omit(j)) goto 60
5847 cc = (txk*xc(j)+tyk*yc(j)+tzk*zc(j))/(bk*b(j))
5848 cc = acos(min(1.0d0,max(-1.0d0,cc)))
5849 td = therk + ther(j)
5851 ! check to see if circles enclose separate regions
5853 if (cc .ge. td) goto 60
5855 ! check for circle J completely inside circle K
5857 if (cc+ther(j) .lt. therk) goto 40
5859 ! check for circles that are essentially parallel
5861 if (cc .gt. delta) goto 50
5866 ! check to see if sphere of interest is completely buried
5869 if (pix2-cc .le. td) goto 170
5875 ! find T value of circle intersections
5878 if (omit(k)) goto 110
5893 ! rotation matrix elements
5905 if (.not. omit(j)) then
5910 ! rotate spheres so K vector colinear with z-axis
5912 uxj = txj*axx + tyj*axy - tzj*axz
5913 uyj = tyj*ayy - txj*ayx
5914 uzj = txj*azx + tyj*azy + tzj*azz
5915 cosine = min(1.0d0,max(-1.0d0,uzj/b(j)))
5916 if (acos(cosine) .lt. therk+ther(j)) then
5917 dsqj = uxj*uxj + uyj*uyj
5922 tr2 = risqk*dsqj - tb*tb
5928 ! get T values of intersection for K circle
5931 tb = min(1.0d0,max(-1.0d0,tb))
5933 if (tyb-txr .lt. 0.0d0) tk1 = pix2 - tk1
5935 tb = min(1.0d0,max(-1.0d0,tb))
5937 if (tyb+txr .lt. 0.0d0) tk2 = pix2 - tk2
5938 thec = (rrsq*uzj-gk*bg(j)) / (rik*ri(j)*b(j))
5939 if (abs(thec) .lt. 1.0d0) then
5941 else if (thec .ge. 1.0d0) then
5943 else if (thec .le. -1.0d0) then
5947 ! see if "tk1" is entry or exit point; check t=0 point;
5948 ! "ti" is exit point, "tf" is entry point
5950 cosine = min(1.0d0,max(-1.0d0, &
5951 (uzj*gk-uxj*rik)/(b(j)*rr)))
5952 if ((acos(cosine)-ther(j))*(tk2-tk1) .le. 0.0d0) then
5960 if (narc .ge. maxarc) then
5962 70 format (/,' SURFATOM -- Increase the Value',&
5966 if (tf .le. ti) then
5987 ! special case; K circle without intersections
5989 if (narc .le. 0) goto 90
5991 ! general case; sum up arclength and set connectivity code
5993 call sort2 (narc,arci,key)
5998 if (narc .gt. 1) then
6001 if (t .lt. arci(j)) then
6002 arcsum = arcsum + arci(j) - t
6003 exang = exang + ex(ni)
6005 if (jb .ge. maxarc) then
6007 80 format (/,' SURFATOM -- Increase the Value',&
6012 kent(jb) = maxarc*i + k
6014 kout(jb) = maxarc*k + i
6023 arcsum = arcsum + pix2 - t
6025 exang = exang + ex(ni)
6028 kent(jb) = maxarc*i + k
6030 kout(jb) = maxarc*k + i
6037 arclen = arclen + gr(k)*arcsum
6040 if (arclen .eq. 0.0d0) goto 170
6041 if (jb .eq. 0) goto 150
6043 ! find number of independent boundaries and check connectivity
6047 if (kout(k) .ne. 0) then
6054 if (m .eq. kent(ii)) then
6057 if (j .eq. jb) goto 150
6069 ! attempt to fix connectivity error by moving atom slightly
6073 140 format (/,' SURFATOM -- Connectivity Error at Atom',i6)
6082 ! compute the exposed surface area for the sphere of interest
6085 area = ib*pix2 + exang + arclen
6086 area = mod(area,4.0d0*pi) * rrsq
6088 ! attempt to fix negative area by moving atom slightly
6090 if (area .lt. 0.0d0) then
6093 160 format (/,' SURFATOM -- Negative Area at Atom',i6)
6104 end subroutine surfatom
6105 !----------------------------------------------------------------
6106 !----------------------------------------------------------------
6107 subroutine alloc_MD_arrays
6108 !EL Allocation of arrays used by MD module
6110 integer :: nres2,nres6
6113 !----------------------
6117 allocate(friction(3,0:nres2),stochforc(3,0:nres2)) !(3,0:MAXRES2)
6118 allocate(fric_work(nres6),stoch_work(nres6),fricgam(nres6)) !(MAXRES6)
6119 if(.not.allocated(fricmat)) allocate(fricmat(nres2,nres2))
6120 allocate(fricvec(nres2,nres2))
6121 allocate(pfric_mat(nres2,nres2),vfric_mat(nres2,nres2))
6122 allocate(afric_mat(nres2,nres2),prand_mat(nres2,nres2))
6123 allocate(vrand_mat1(nres2,nres2),vrand_mat2(nres2,nres2)) !(MAXRES2,MAXRES2)
6124 allocate(pfric0_mat(nres2,nres2,0:maxflag_stoch))
6125 allocate(afric0_mat(nres2,nres2,0:maxflag_stoch))
6126 allocate(vfric0_mat(nres2,nres2,0:maxflag_stoch))
6127 allocate(prand0_mat(nres2,nres2,0:maxflag_stoch))
6128 allocate(vrand0_mat1(nres2,nres2,0:maxflag_stoch))
6129 allocate(vrand0_mat2(nres2,nres2,0:maxflag_stoch)) !(MAXRES2,MAXRES2,0:maxflag_stoch)
6130 allocate(flag_stoch(0:maxflag_stoch)) !(0:maxflag_stoch)
6132 allocate(mt1(nres2,nres2),mt2(nres2,nres2),mt3(nres2,nres2)) !(maxres2,maxres2)
6133 !----------------------
6135 ! commom.langevin.lang0
6137 allocate(friction(3,0:nres2),stochforc(3,0:nres2)) !(3,0:MAXRES2)
6138 if(.not.allocated(fricmat)) allocate(fricmat(nres2,nres2))
6139 allocate(fricvec(nres2,nres2)) !(MAXRES2,MAXRES2)
6140 allocate(fric_work(nres6),stoch_work(nres6),fricgam(nres6)) !(MAXRES6)
6141 allocate(flag_stoch(0:maxflag_stoch)) !(0:maxflag_stoch)
6144 if(.not.allocated(fcopy)) allocate(fcopy(nres2,nres2))
6145 !----------------------
6146 ! commom.hairpin in CSA module
6147 !----------------------
6148 ! common.mce in MCM_MD module
6149 !----------------------
6151 ! common /mdgrad/ in module.energy
6152 ! common /back_constr/ in module.energy
6153 ! common /qmeas/ in module.energy
6156 allocate(potEcomp(0:n_ene+4)) !(0:n_ene+4)
6158 allocate(d_t(3,0:nres2),d_a(3,0:nres2),d_t_old(3,0:nres2)) !(3,0:MAXRES2)
6159 allocate(d_a_work(nres6)) !(6*MAXRES)
6161 allocate(DM(nres2),DU1(nres2),DU2(nres2))
6162 allocate(DMorig(nres2),DU1orig(nres2),DU2orig(nres2))
6164 write (iout,*) "Before A Allocation",nfgtasks-1
6166 allocate(Gmat(nres2,nres2),A(nres2,nres2))
6167 if(.not.allocated(Ginv)) allocate(Ginv(nres2,nres2)) !in control: ergastulum
6168 allocate(Gsqrp(nres2,nres2),Gsqrm(nres2,nres2),Gvec(nres2,nres2)) !(maxres2,maxres2)
6170 allocate(Geigen(nres2)) !(maxres2)
6171 if(.not.allocated(vtot)) allocate(vtot(nres2)) !(maxres2)
6172 ! common /inertia/ in io_conf: parmread
6173 ! real(kind=8),dimension(:),allocatable :: ISC,msc !(ntyp+1)
6174 ! common /langevin/in io read_MDpar
6175 ! real(kind=8),dimension(:),allocatable :: gamsc !(ntyp1)
6176 ! real(kind=8),dimension(:),allocatable :: stdfsc !(ntyp)
6177 ! in io_conf: parmread
6178 ! real(kind=8),dimension(:),allocatable :: restok !(ntyp+1)
6179 ! common /mdpmpi/ in control: ergastulum
6180 if(.not.allocated(ng_start)) allocate(ng_start(0:nfgtasks-1))
6181 if(.not.allocated(ng_counts)) allocate(ng_counts(0:nfgtasks-1))
6182 if(.not.allocated(nginv_counts)) allocate(nginv_counts(0:nfgtasks-1)) !(0:MaxProcs-1)
6183 if(.not.allocated(nginv_start)) allocate(nginv_start(0:nfgtasks)) !(0:MaxProcs)
6184 !----------------------
6185 ! common.muca in read_muca
6186 ! common /double_muca/
6187 ! real(kind=8) :: elow,ehigh,factor,hbin,factor_min
6188 ! real(kind=8),dimension(:),allocatable :: emuca,nemuca,&
6189 ! nemuca2,hist !(4*maxres)
6190 ! common /integer_muca/
6191 ! integer :: nmuca,imtime,muca_smooth
6193 ! real(kind=8),dimension(:),allocatable :: elowi,ehighi !(maxprocs)
6194 !----------------------
6196 ! common /mdgrad/ in module.energy
6197 ! common /back_constr/ in module.energy
6198 ! common /qmeas/ in module.energy
6202 allocate(d_t_work(nres6),d_t_work_new(nres6),d_af_work(nres6))
6203 allocate(d_as_work(nres6),kinetic_force(nres6)) !(MAXRES6)
6204 allocate(d_t_new(3,0:nres2),d_a_old(3,0:nres2),d_a_short(3,0:nres2)) !,d_a !(3,0:MAXRES2)
6205 allocate(stdforcp(nres),stdforcsc(nres)) !(MAXRES)
6206 !----------------------
6208 allocate(D_ban(nres6)) !(MAXRES6) maxres6=6*maxres
6209 ! common /stochcalc/ stochforcvec
6210 allocate(stochforcvec(nres6)) !(MAXRES6) maxres6=6*maxres
6211 !----------------------
6213 end subroutine alloc_MD_arrays
6214 !-----------------------------------------------------------------------------
6215 !-----------------------------------------------------------------------------