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)
2510 if ((.not.rest).and.(indpdb.eq.0)) then
2512 if(iranconf.ne.0) 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 call etotal(potEcomp)
2554 if (large) call enerprint(potEcomp)
2557 t_etotal=t_etotal+MPI_Wtime()-tt0
2559 t_etotal=t_etotal+tcpu()-tt0
2566 if (amax*d_time .gt. dvmax) then
2567 d_time=d_time*dvmax/amax
2568 if(me.eq.king.or..not.out1file) write (iout,*) &
2569 "Time step reduced to",d_time,&
2570 " because of too large initial acceleration."
2572 if(me.eq.king.or..not.out1file)then
2573 write(iout,*) "Potential energy and its components"
2574 call enerprint(potEcomp)
2575 ! write(iout,*) (potEcomp(i),i=0,n_ene)
2577 potE=potEcomp(0)-potEcomp(20)
2580 if (ntwe.ne.0) call statout(itime)
2581 if(me.eq.king.or..not.out1file) &
2582 write (iout,'(/a/3(a25,1pe14.5/))') "Initial:", &
2583 " Kinetic energy",EK," Potential energy",potE, &
2584 " Total energy",totE," Maximum acceleration ", &
2587 write (iout,*) "Initial coordinates"
2589 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(c(j,i),j=1,3),&
2592 write (iout,*) "Initial dC"
2594 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(dc(j,i),j=1,3),&
2595 (dc(j,i+nres),j=1,3)
2597 write (iout,*) "Initial velocities"
2598 write (iout,"(13x,' backbone ',23x,' side chain')")
2600 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),&
2601 (d_t(j,i+nres),j=1,3)
2603 write (iout,*) "Initial accelerations"
2605 ! write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_a(j,i),j=1,3),
2606 write (iout,'(i3,3f15.10,3x,3f15.10)') i,(d_a(j,i),j=1,3),&
2607 (d_a(j,i+nres),j=1,3)
2613 d_t_old(j,i)=d_t(j,i)
2614 d_a_old(j,i)=d_a(j,i)
2616 ! write (iout,*) "dc_old",i,(dc_old(j,i),j=1,3)
2625 call etotal_short(energia_short)
2626 if (large) call enerprint(potEcomp)
2629 t_eshort=t_eshort+MPI_Wtime()-tt0
2631 t_eshort=t_eshort+tcpu()-tt0
2636 if(.not.out1file .and. large) then
2637 write (iout,*) "energia_long",energia_long(0),&
2638 " energia_short",energia_short(0),&
2639 " total",energia_long(0)+energia_short(0)
2640 write (iout,*) "Initial fast-force accelerations"
2642 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_a(j,i),j=1,3),&
2643 (d_a(j,i+nres),j=1,3)
2646 ! 7/2/2009 Copy accelerations due to short-lange forces to an auxiliary array
2649 d_a_short(j,i)=d_a(j,i)
2658 call etotal_long(energia_long)
2659 if (large) call enerprint(potEcomp)
2662 t_elong=t_elong+MPI_Wtime()-tt0
2664 t_elong=t_elong+tcpu()-tt0
2669 if(.not.out1file .and. large) then
2670 write (iout,*) "energia_long",energia_long(0)
2671 write (iout,*) "Initial slow-force accelerations"
2673 write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_a(j,i),j=1,3),&
2674 (d_a(j,i+nres),j=1,3)
2678 t_enegrad=t_enegrad+MPI_Wtime()-tt0
2680 t_enegrad=t_enegrad+tcpu()-tt0
2684 end subroutine init_MD
2685 !-----------------------------------------------------------------------------
2686 subroutine random_vel
2688 ! implicit real*8 (a-h,o-z)
2690 use random, only:anorm_distr
2692 ! include 'DIMENSIONS'
2693 ! include 'COMMON.CONTROL'
2694 ! include 'COMMON.VAR'
2695 ! include 'COMMON.MD'
2697 ! include 'COMMON.LANGEVIN'
2699 ! include 'COMMON.LANGEVIN.lang0'
2701 ! include 'COMMON.CHAIN'
2702 ! include 'COMMON.DERIV'
2703 ! include 'COMMON.GEO'
2704 ! include 'COMMON.LOCAL'
2705 ! include 'COMMON.INTERACT'
2706 ! include 'COMMON.IOUNITS'
2707 ! include 'COMMON.NAMES'
2708 ! include 'COMMON.TIME1'
2709 real(kind=8) :: xv,sigv,lowb,highb ,Ek1
2712 real(kind=8) ,allocatable, dimension(:) :: DDU1,DDU2,DL2,DL1,xsolv,DML,rs
2713 real(kind=8) :: sumx
2715 real(kind=8) ,allocatable, dimension(:) :: rsold
2716 real (kind=8),allocatable,dimension(:,:) :: matold
2720 integer :: i,j,ii,k,ind,mark,imark,mnum
2721 ! Generate random velocities from Gaussian distribution of mean 0 and std of KT/m
2722 ! First generate velocities in the eigenspace of the G matrix
2723 ! write (iout,*) "Calling random_vel dimen dimen3",dimen,dimen3
2730 sigv=dsqrt((Rb*t_bath)/geigen(i))
2733 d_t_work_new(ii)=anorm_distr(xv,sigv,lowb,highb)
2735 write (iout,*) "i",i," ii",ii," geigen",geigen(i),&
2736 " d_t_work_new",d_t_work_new(ii)
2747 Ek1=Ek1+0.5d0*geigen(i)*d_t_work_new(ii)**2
2750 write (iout,*) "Ek from eigenvectors",Ek1
2751 write (iout,*) "Kinetic temperatures",2*Ek1/(3*dimen*Rb)
2755 ! Transform velocities to UNRES coordinate space
2756 allocate (DL1(2*nres))
2757 allocate (DDU1(2*nres))
2758 allocate (DL2(2*nres))
2759 allocate (DDU2(2*nres))
2760 allocate (xsolv(2*nres))
2761 allocate (DML(2*nres))
2762 allocate (rs(2*nres))
2764 allocate (rsold(2*nres))
2765 allocate (matold(2*nres,2*nres))
2767 matold(1,1)=DMorig(1)
2768 matold(1,2)=DU1orig(1)
2769 matold(1,3)=DU2orig(1)
2770 write (*,*) DMorig(1),DU1orig(1),DU2orig(1)
2775 matold(i,j)=DMorig(i)
2776 matold(i,j-1)=DU1orig(i-1)
2778 matold(i,j-2)=DU2orig(i-2)
2786 matold(i,j+1)=DU1orig(i)
2792 matold(i,j+2)=DU2orig(i)
2796 matold(dimen,dimen)=DMorig(dimen)
2797 matold(dimen,dimen-1)=DU1orig(dimen-1)
2798 matold(dimen,dimen-2)=DU2orig(dimen-2)
2799 write(iout,*) "old gmatrix"
2800 call matout(dimen,dimen,2*nres,2*nres,matold)
2804 ! Find the ith eigenvector of the pentadiagonal inertiq matrix
2808 DML(j)=DMorig(j)-geigen(i)
2811 DML(j-1)=DMorig(j)-geigen(i)
2816 DDU1(imark-1)=DU2orig(imark-1)
2817 do j=imark+1,dimen-1
2818 DDU1(j-1)=DU1orig(j)
2826 DDU2(j)=DU2orig(j+1)
2835 write (iout,*) "DL2,DL1,DML,DDU1,DDU2"
2836 write(iout,'(10f10.5)') (DL2(k),k=3,dimen-1)
2837 write(iout,'(10f10.5)') (DL1(k),k=2,dimen-1)
2838 write(iout,'(10f10.5)') (DML(k),k=1,dimen-1)
2839 write(iout,'(10f10.5)') (DDU1(k),k=1,dimen-2)
2840 write(iout,'(10f10.5)') (DDU2(k),k=1,dimen-3)
2843 if (imark.gt.2) rs(imark-2)=-DU2orig(imark-2)
2844 if (imark.gt.1) rs(imark-1)=-DU1orig(imark-1)
2845 if (imark.lt.dimen) rs(imark)=-DU1orig(imark)
2846 if (imark.lt.dimen-1) rs(imark+1)=-DU2orig(imark)
2850 ! write (iout,*) "Vector rs"
2852 ! write (iout,*) j,rs(j)
2855 call FDIAG(dimen-1,DL2,DL1,DML,DDU1,DDU2,rs,xsolv,mark)
2862 sumx=-geigen(i)*xsolv(j)
2864 sumx=sumx+matold(j,k)*xsolv(k)
2867 sumx=sumx+matold(j,k)*xsolv(k-1)
2869 write(iout,'(i5,3f10.5)') j,sumx,rsold(j),sumx-rsold(j)
2872 sumx=-geigen(i)*xsolv(j-1)
2874 sumx=sumx+matold(j,k)*xsolv(k)
2877 sumx=sumx+matold(j,k)*xsolv(k-1)
2879 write(iout,'(i5,3f10.5)') j-1,sumx,rsold(j-1),sumx-rsold(j-1)
2883 "Solution of equations system",i," for eigenvalue",geigen(i)
2885 write(iout,'(i5,f10.5)') j,xsolv(j)
2888 do j=dimen-1,imark,-1
2893 write (iout,*) "Un-normalized eigenvector",i," for eigenvalue",geigen(i)
2895 write(iout,'(i5,f10.5)') j,xsolv(j)
2898 ! Normalize ith eigenvector
2901 sumx=sumx+xsolv(j)**2
2905 xsolv(j)=xsolv(j)/sumx
2908 write (iout,*) "Eigenvector",i," for eigenvalue",geigen(i)
2910 write(iout,'(i5,3f10.5)') j,xsolv(j)
2913 ! All done at this point for eigenvector i, exit loop
2921 write (iout,*) "Unable to find eigenvector",i
2924 ! write (iout,*) "i=",i
2926 ! write (iout,*) "k=",k
2929 ! write(iout,*) "ind",ind," ind1",3*(i-1)+k
2930 d_t_work(ind)=d_t_work(ind) &
2931 +xsolv(j)*d_t_work_new(3*(i-1)+k)
2934 enddo ! i (loop over the eigenvectors)
2937 write (iout,*) "d_t_work"
2939 write (iout,"(i5,f10.5)") i,d_t_work(i)
2944 ! if (itype(i,1).eq.10) then
2946 if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
2947 iti=iabs(itype(i,mnum))
2948 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
2949 if (itype(i,1).eq.10 .or. itype(i,mnum).eq.ntyp1_molec(mnum)&
2950 .or.(mnum.eq.5)) then
2957 ! write (iout,*) "k",k," ii+k",ii+k," ii+j+k",ii+j+k,"EK1",Ek1
2958 Ek1=Ek1+0.5d0*mp(mnum)*((d_t_work(ii+j+k)+d_t_work_new(ii+k))/2)**2+&
2959 0.5d0*0.25d0*IP(mnum)*(d_t_work(ii+j+k)-d_t_work_new(ii+k))**2
2962 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
2963 .and.(mnum.ne.5)) ii=ii+3
2964 write (iout,*) "i",i," itype",itype(i,mnum)," mass",msc(itype(i,mnum),mnum)
2965 write (iout,*) "ii",ii
2968 write (iout,*) "k",k," ii",ii,"EK1",EK1
2969 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
2971 Ek1=Ek1+0.5d0*Isc(iabs(itype(i,mnum)),mnum)*(d_t_work(ii)-d_t_work(ii-3))**2
2972 Ek1=Ek1+0.5d0*msc(iabs(itype(i,mnum)),mnum)*d_t_work(ii)**2
2974 write (iout,*) "i",i," ii",ii
2976 write (iout,*) "Ek from d_t_work",Ek1
2977 write (iout,*) "Kinetic temperatures",2*Ek1/(3*dimen*Rb)
2993 d_t(k,j)=d_t_work(ind)
2997 if (itype(j,1).ne.10 .and. itype(j,mnum).ne.ntyp1_molec(mnum)&
2998 .and.(mnum.ne.5)) then
3000 d_t(k,j+nres)=d_t_work(ind)
3006 write (iout,*) "Random velocities in the Calpha,SC space"
3008 write (iout,'(i3,3f10.5)') i,(d_t(j,i),j=1,3)
3011 write (iout,'(i3,3f10.5)') i,(d_t(j,i+nres),j=1,3)
3018 ! if (itype(i,1).eq.10) then
3020 if (itype(i,1).eq.10 .or. itype(i,mnum).eq.ntyp1_molec(mnum)&
3021 .or.(mnum.eq.5)) then
3023 d_t(j,i)=d_t(j,i+1)-d_t(j,i)
3027 d_t(j,i+nres)=d_t(j,i+nres)-d_t(j,i)
3028 d_t(j,i)=d_t(j,i+1)-d_t(j,i)
3033 write (iout,*)"Random velocities in the virtual-bond-vector space"
3035 write (iout,'(i3,3f10.5)') i,(d_t(j,i),j=1,3)
3038 write (iout,'(i3,3f10.5)') i,(d_t(j,i+nres),j=1,3)
3041 write (iout,*) "Ek from d_t_work",Ek1
3042 write (iout,*) "Kinetic temperatures",2*Ek1/(3*dimen*Rb)
3050 d_t_work(ind)=d_t_work(ind) &
3051 +Gvec(i,j)*d_t_work_new((j-1)*3+k+1)
3053 ! write (iout,*) "i",i," ind",ind," d_t_work",d_t_work(ind)
3057 ! Transfer to the d_t vector
3059 d_t(j,0)=d_t_work(j)
3065 d_t(j,i)=d_t_work(ind)
3070 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
3071 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
3072 .and.(mnum.ne.5)) then
3075 d_t(j,i+nres)=d_t_work(ind)
3081 ! write (iout,*) "Kinetic energy",Ek,EK1," kinetic temperature",&
3082 ! 2.0d0/(dimen3*Rb)*EK,2.0d0/(dimen3*Rb)*EK1
3084 ! write(iout,*) "end init MD"
3086 end subroutine random_vel
3087 !-----------------------------------------------------------------------------
3089 subroutine sd_verlet_p_setup
3090 ! Sets up the parameters of stochastic Verlet algorithm
3091 ! implicit real*8 (a-h,o-z)
3092 ! include 'DIMENSIONS'
3093 use control, only: tcpu
3098 ! include 'COMMON.CONTROL'
3099 ! include 'COMMON.VAR'
3100 ! include 'COMMON.MD'
3102 ! include 'COMMON.LANGEVIN'
3104 ! include 'COMMON.LANGEVIN.lang0'
3106 ! include 'COMMON.CHAIN'
3107 ! include 'COMMON.DERIV'
3108 ! include 'COMMON.GEO'
3109 ! include 'COMMON.LOCAL'
3110 ! include 'COMMON.INTERACT'
3111 ! include 'COMMON.IOUNITS'
3112 ! include 'COMMON.NAMES'
3113 ! include 'COMMON.TIME1'
3114 real(kind=8),dimension(6*nres) :: emgdt !(MAXRES6) maxres6=6*maxres
3115 real(kind=8) :: pterm,vterm,rho,rhoc,vsig
3116 real(kind=8),dimension(6*nres) :: pfric_vec,vfric_vec,afric_vec,&
3117 prand_vec,vrand_vec1,vrand_vec2 !(MAXRES6) maxres6=6*maxres
3118 logical :: lprn = .false.
3119 real(kind=8) :: zero = 1.0d-8, gdt_radius = 0.05d0
3120 real(kind=8) :: ktm,gdt,egdt,gdt2,gdt3,gdt4,gdt5,gdt6,gdt7,gdt8,&
3122 integer :: i,maxres2
3129 ! AL 8/17/04 Code adapted from tinker
3131 ! Get the frictional and random terms for stochastic dynamics in the
3132 ! eigenspace of mass-scaled UNRES friction matrix
3136 gdt = fricgam(i) * d_time
3138 ! Stochastic dynamics reduces to simple MD for zero friction
3140 if (gdt .le. zero) then
3141 pfric_vec(i) = 1.0d0
3142 vfric_vec(i) = d_time
3143 afric_vec(i) = 0.5d0 * d_time * d_time
3144 prand_vec(i) = 0.0d0
3145 vrand_vec1(i) = 0.0d0
3146 vrand_vec2(i) = 0.0d0
3148 ! Analytical expressions when friction coefficient is large
3151 if (gdt .ge. gdt_radius) then
3154 vfric_vec(i) = (1.0d0-egdt) / fricgam(i)
3155 afric_vec(i) = (d_time-vfric_vec(i)) / fricgam(i)
3156 pterm = 2.0d0*gdt - 3.0d0 + (4.0d0-egdt)*egdt
3157 vterm = 1.0d0 - egdt**2
3158 rho = (1.0d0-egdt)**2 / sqrt(pterm*vterm)
3160 ! Use series expansions when friction coefficient is small
3171 afric_vec(i) = (gdt2/2.0d0 - gdt3/6.0d0 + gdt4/24.0d0 &
3172 - gdt5/120.0d0 + gdt6/720.0d0 &
3173 - gdt7/5040.0d0 + gdt8/40320.0d0 &
3174 - gdt9/362880.0d0) / fricgam(i)**2
3175 vfric_vec(i) = d_time - fricgam(i)*afric_vec(i)
3176 pfric_vec(i) = 1.0d0 - fricgam(i)*vfric_vec(i)
3177 pterm = 2.0d0*gdt3/3.0d0 - gdt4/2.0d0 &
3178 + 7.0d0*gdt5/30.0d0 - gdt6/12.0d0 &
3179 + 31.0d0*gdt7/1260.0d0 - gdt8/160.0d0 &
3180 + 127.0d0*gdt9/90720.0d0
3181 vterm = 2.0d0*gdt - 2.0d0*gdt2 + 4.0d0*gdt3/3.0d0 &
3182 - 2.0d0*gdt4/3.0d0 + 4.0d0*gdt5/15.0d0 &
3183 - 4.0d0*gdt6/45.0d0 + 8.0d0*gdt7/315.0d0 &
3184 - 2.0d0*gdt8/315.0d0 + 4.0d0*gdt9/2835.0d0
3185 rho = sqrt(3.0d0) * (0.5d0 - 3.0d0*gdt/16.0d0 &
3186 - 17.0d0*gdt2/1280.0d0 &
3187 + 17.0d0*gdt3/6144.0d0 &
3188 + 40967.0d0*gdt4/34406400.0d0 &
3189 - 57203.0d0*gdt5/275251200.0d0 &
3190 - 1429487.0d0*gdt6/13212057600.0d0)
3193 ! Compute the scaling factors of random terms for the nonzero friction case
3195 ktm = 0.5d0*d_time/fricgam(i)
3196 psig = dsqrt(ktm*pterm) / fricgam(i)
3197 vsig = dsqrt(ktm*vterm)
3198 rhoc = dsqrt(1.0d0 - rho*rho)
3200 vrand_vec1(i) = vsig * rho
3201 vrand_vec2(i) = vsig * rhoc
3206 "pfric_vec, vfric_vec, afric_vec, prand_vec, vrand_vec1,",&
3209 write (iout,'(i5,6e15.5)') i,pfric_vec(i),vfric_vec(i),&
3210 afric_vec(i),prand_vec(i),vrand_vec1(i),vrand_vec2(i)
3214 ! Transform from the eigenspace of mass-scaled friction matrix to UNRES variables
3217 call eigtransf(dimen,maxres2,mt3,mt2,pfric_vec,pfric_mat)
3218 call eigtransf(dimen,maxres2,mt3,mt2,vfric_vec,vfric_mat)
3219 call eigtransf(dimen,maxres2,mt3,mt2,afric_vec,afric_mat)
3220 call eigtransf(dimen,maxres2,mt3,mt1,prand_vec,prand_mat)
3221 call eigtransf(dimen,maxres2,mt3,mt1,vrand_vec1,vrand_mat1)
3222 call eigtransf(dimen,maxres2,mt3,mt1,vrand_vec2,vrand_mat2)
3225 t_sdsetup=t_sdsetup+MPI_Wtime()
3227 t_sdsetup=t_sdsetup+tcpu()-tt0
3230 end subroutine sd_verlet_p_setup
3231 !-----------------------------------------------------------------------------
3232 subroutine eigtransf1(n,ndim,ab,d,c)
3236 real(kind=8) :: ab(ndim,ndim,n),c(ndim,n),d(ndim)
3242 c(i,j)=c(i,j)+ab(k,j,i)*d(k)
3247 end subroutine eigtransf1
3248 !-----------------------------------------------------------------------------
3249 subroutine eigtransf(n,ndim,a,b,d,c)
3253 real(kind=8) :: a(ndim,n),b(ndim,n),c(ndim,n),d(ndim)
3259 c(i,j)=c(i,j)+a(i,k)*b(k,j)*d(k)
3264 end subroutine eigtransf
3265 !-----------------------------------------------------------------------------
3266 subroutine sd_verlet1
3268 ! Applying stochastic velocity Verlet algorithm - step 1 to velocities
3270 ! implicit real*8 (a-h,o-z)
3271 ! include 'DIMENSIONS'
3272 ! include 'COMMON.CONTROL'
3273 ! include 'COMMON.VAR'
3274 ! include 'COMMON.MD'
3276 ! include 'COMMON.LANGEVIN'
3278 ! include 'COMMON.LANGEVIN.lang0'
3280 ! include 'COMMON.CHAIN'
3281 ! include 'COMMON.DERIV'
3282 ! include 'COMMON.GEO'
3283 ! include 'COMMON.LOCAL'
3284 ! include 'COMMON.INTERACT'
3285 ! include 'COMMON.IOUNITS'
3286 ! include 'COMMON.NAMES'
3287 !el real(kind=8),dimension(6*nres) :: stochforcvec !(MAXRES6) maxres6=6*maxres
3288 !el common /stochcalc/ stochforcvec
3289 logical :: lprn = .false.
3290 real(kind=8) :: ddt1,ddt2
3291 integer :: i,j,ind,inres
3293 ! write (iout,*) "dc_old"
3295 ! write (iout,'(i5,3f10.5,5x,3f10.5)')
3296 ! & i,(dc_old(j,i),j=1,3),(dc_old(j,i+nres),j=1,3)
3299 dc_work(j)=dc_old(j,0)
3300 d_t_work(j)=d_t_old(j,0)
3301 d_a_work(j)=d_a_old(j,0)
3306 dc_work(ind+j)=dc_old(j,i)
3307 d_t_work(ind+j)=d_t_old(j,i)
3308 d_a_work(ind+j)=d_a_old(j,i)
3314 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
3315 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
3316 .and.(mnum.ne.5)) then
3318 dc_work(ind+j)=dc_old(j,i+nres)
3319 d_t_work(ind+j)=d_t_old(j,i+nres)
3320 d_a_work(ind+j)=d_a_old(j,i+nres)
3328 "pfric_mat, vfric_mat, afric_mat, prand_mat, vrand_mat1,",&
3332 write (iout,'(2i5,6e15.5)') i,j,pfric_mat(i,j),&
3333 vfric_mat(i,j),afric_mat(i,j),&
3334 prand_mat(i,j),vrand_mat1(i,j),vrand_mat2(i,j)
3342 dc_work(i)=dc_work(i)+vfric_mat(i,j)*d_t_work(j) &
3343 +afric_mat(i,j)*d_a_work(j)+prand_mat(i,j)*stochforcvec(j)
3344 ddt1=ddt1+pfric_mat(i,j)*d_t_work(j)
3345 ddt2=ddt2+vfric_mat(i,j)*d_a_work(j)
3347 d_t_work_new(i)=ddt1+0.5d0*ddt2
3348 d_t_work(i)=ddt1+ddt2
3353 d_t(j,0)=d_t_work(j)
3358 dc(j,i)=dc_work(ind+j)
3359 d_t(j,i)=d_t_work(ind+j)
3365 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
3366 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
3367 .and.(mnum.ne.5)) then
3370 dc(j,inres)=dc_work(ind+j)
3371 d_t(j,inres)=d_t_work(ind+j)
3377 end subroutine sd_verlet1
3378 !-----------------------------------------------------------------------------
3379 subroutine sd_verlet2
3381 ! Calculating the adjusted velocities for accelerations
3383 ! implicit real*8 (a-h,o-z)
3384 ! include 'DIMENSIONS'
3385 ! include 'COMMON.CONTROL'
3386 ! include 'COMMON.VAR'
3387 ! include 'COMMON.MD'
3389 ! include 'COMMON.LANGEVIN'
3391 ! include 'COMMON.LANGEVIN.lang0'
3393 ! include 'COMMON.CHAIN'
3394 ! include 'COMMON.DERIV'
3395 ! include 'COMMON.GEO'
3396 ! include 'COMMON.LOCAL'
3397 ! include 'COMMON.INTERACT'
3398 ! include 'COMMON.IOUNITS'
3399 ! include 'COMMON.NAMES'
3400 !el real(kind=8),dimension(6*nres) :: stochforcvec,stochforcvecV !(MAXRES6) maxres6=6*maxres
3401 real(kind=8),dimension(6*nres) :: stochforcvecV !(MAXRES6) maxres6=6*maxres
3402 !el common /stochcalc/ stochforcvec
3404 real(kind=8) :: ddt1,ddt2
3405 integer :: i,j,ind,inres
3406 ! Compute the stochastic forces which contribute to velocity change
3408 call stochastic_force(stochforcvecV)
3415 ddt1=ddt1+vfric_mat(i,j)*d_a_work(j)
3416 ddt2=ddt2+vrand_mat1(i,j)*stochforcvec(j)+ &
3417 vrand_mat2(i,j)*stochforcvecV(j)
3419 d_t_work(i)=d_t_work_new(i)+0.5d0*ddt1+ddt2
3423 d_t(j,0)=d_t_work(j)
3428 d_t(j,i)=d_t_work(ind+j)
3434 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
3435 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
3436 .and.(mnum.ne.5)) then
3439 d_t(j,inres)=d_t_work(ind+j)
3445 end subroutine sd_verlet2
3446 !-----------------------------------------------------------------------------
3447 subroutine sd_verlet_ciccotti_setup
3449 ! Sets up the parameters of stochastic velocity Verlet algorithmi; Ciccotti's
3451 ! implicit real*8 (a-h,o-z)
3452 ! include 'DIMENSIONS'
3453 use control, only: tcpu
3458 ! include 'COMMON.CONTROL'
3459 ! include 'COMMON.VAR'
3460 ! include 'COMMON.MD'
3462 ! include 'COMMON.LANGEVIN'
3464 ! include 'COMMON.LANGEVIN.lang0'
3466 ! include 'COMMON.CHAIN'
3467 ! include 'COMMON.DERIV'
3468 ! include 'COMMON.GEO'
3469 ! include 'COMMON.LOCAL'
3470 ! include 'COMMON.INTERACT'
3471 ! include 'COMMON.IOUNITS'
3472 ! include 'COMMON.NAMES'
3473 ! include 'COMMON.TIME1'
3474 real(kind=8),dimension(6*nres) :: emgdt !(MAXRES6) maxres6=6*maxres
3475 real(kind=8) :: pterm,vterm,rho,rhoc,vsig
3476 real(kind=8),dimension(6*nres) :: pfric_vec,vfric_vec,afric_vec,&
3477 prand_vec,vrand_vec1,vrand_vec2 !(MAXRES6) maxres6=6*maxres
3478 logical :: lprn = .false.
3479 real(kind=8) :: zero = 1.0d-8, gdt_radius = 0.05d0
3480 real(kind=8) :: ktm,gdt,egdt,tt0
3481 integer :: i,maxres2
3488 ! AL 8/17/04 Code adapted from tinker
3490 ! Get the frictional and random terms for stochastic dynamics in the
3491 ! eigenspace of mass-scaled UNRES friction matrix
3495 write (iout,*) "i",i," fricgam",fricgam(i)
3496 gdt = fricgam(i) * d_time
3498 ! Stochastic dynamics reduces to simple MD for zero friction
3500 if (gdt .le. zero) then
3501 pfric_vec(i) = 1.0d0
3502 vfric_vec(i) = d_time
3503 afric_vec(i) = 0.5d0*d_time*d_time
3504 prand_vec(i) = afric_vec(i)
3505 vrand_vec2(i) = vfric_vec(i)
3507 ! Analytical expressions when friction coefficient is large
3512 vfric_vec(i) = dexp(-0.5d0*gdt)*d_time
3513 afric_vec(i) = 0.5d0*dexp(-0.25d0*gdt)*d_time*d_time
3514 prand_vec(i) = afric_vec(i)
3515 vrand_vec2(i) = vfric_vec(i)
3517 ! Compute the scaling factors of random terms for the nonzero friction case
3519 ! ktm = 0.5d0*d_time/fricgam(i)
3520 ! psig = dsqrt(ktm*pterm) / fricgam(i)
3521 ! vsig = dsqrt(ktm*vterm)
3522 ! prand_vec(i) = psig*afric_vec(i)
3523 ! vrand_vec2(i) = vsig*vfric_vec(i)
3528 "pfric_vec, vfric_vec, afric_vec, prand_vec, vrand_vec1,",&
3531 write (iout,'(i5,6e15.5)') i,pfric_vec(i),vfric_vec(i),&
3532 afric_vec(i),prand_vec(i),vrand_vec1(i),vrand_vec2(i)
3536 ! Transform from the eigenspace of mass-scaled friction matrix to UNRES variables
3538 call eigtransf(dimen,maxres2,mt3,mt2,pfric_vec,pfric_mat)
3539 call eigtransf(dimen,maxres2,mt3,mt2,vfric_vec,vfric_mat)
3540 call eigtransf(dimen,maxres2,mt3,mt2,afric_vec,afric_mat)
3541 call eigtransf(dimen,maxres2,mt3,mt1,prand_vec,prand_mat)
3542 call eigtransf(dimen,maxres2,mt3,mt1,vrand_vec2,vrand_mat2)
3544 t_sdsetup=t_sdsetup+MPI_Wtime()
3546 t_sdsetup=t_sdsetup+tcpu()-tt0
3549 end subroutine sd_verlet_ciccotti_setup
3550 !-----------------------------------------------------------------------------
3551 subroutine sd_verlet1_ciccotti
3553 ! Applying stochastic velocity Verlet algorithm - step 1 to velocities
3554 ! implicit real*8 (a-h,o-z)
3556 ! include 'DIMENSIONS'
3560 ! include 'COMMON.CONTROL'
3561 ! include 'COMMON.VAR'
3562 ! include 'COMMON.MD'
3564 ! include 'COMMON.LANGEVIN'
3566 ! include 'COMMON.LANGEVIN.lang0'
3568 ! include 'COMMON.CHAIN'
3569 ! include 'COMMON.DERIV'
3570 ! include 'COMMON.GEO'
3571 ! include 'COMMON.LOCAL'
3572 ! include 'COMMON.INTERACT'
3573 ! include 'COMMON.IOUNITS'
3574 ! include 'COMMON.NAMES'
3575 !el real(kind=8),dimension(6*nres) :: stochforcvec !(MAXRES6) maxres6=6*maxres
3576 !el common /stochcalc/ stochforcvec
3577 logical :: lprn = .false.
3578 real(kind=8) :: ddt1,ddt2
3579 integer :: i,j,ind,inres
3580 ! write (iout,*) "dc_old"
3582 ! write (iout,'(i5,3f10.5,5x,3f10.5)')
3583 ! & i,(dc_old(j,i),j=1,3),(dc_old(j,i+nres),j=1,3)
3586 dc_work(j)=dc_old(j,0)
3587 d_t_work(j)=d_t_old(j,0)
3588 d_a_work(j)=d_a_old(j,0)
3593 dc_work(ind+j)=dc_old(j,i)
3594 d_t_work(ind+j)=d_t_old(j,i)
3595 d_a_work(ind+j)=d_a_old(j,i)
3600 if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
3602 dc_work(ind+j)=dc_old(j,i+nres)
3603 d_t_work(ind+j)=d_t_old(j,i+nres)
3604 d_a_work(ind+j)=d_a_old(j,i+nres)
3613 "pfric_mat, vfric_mat, afric_mat, prand_mat, vrand_mat1,",&
3617 write (iout,'(2i5,6e15.5)') i,j,pfric_mat(i,j),&
3618 vfric_mat(i,j),afric_mat(i,j),&
3619 prand_mat(i,j),vrand_mat1(i,j),vrand_mat2(i,j)
3627 dc_work(i)=dc_work(i)+vfric_mat(i,j)*d_t_work(j) &
3628 +afric_mat(i,j)*d_a_work(j)+prand_mat(i,j)*stochforcvec(j)
3629 ddt1=ddt1+pfric_mat(i,j)*d_t_work(j)
3630 ddt2=ddt2+vfric_mat(i,j)*d_a_work(j)
3632 d_t_work_new(i)=ddt1+0.5d0*ddt2
3633 d_t_work(i)=ddt1+ddt2
3638 d_t(j,0)=d_t_work(j)
3643 dc(j,i)=dc_work(ind+j)
3644 d_t(j,i)=d_t_work(ind+j)
3650 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
3651 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
3652 .and.(mnum.ne.5)) then
3655 dc(j,inres)=dc_work(ind+j)
3656 d_t(j,inres)=d_t_work(ind+j)
3662 end subroutine sd_verlet1_ciccotti
3663 !-----------------------------------------------------------------------------
3664 subroutine sd_verlet2_ciccotti
3666 ! Calculating the adjusted velocities for accelerations
3668 ! implicit real*8 (a-h,o-z)
3669 ! include 'DIMENSIONS'
3670 ! include 'COMMON.CONTROL'
3671 ! include 'COMMON.VAR'
3672 ! include 'COMMON.MD'
3674 ! include 'COMMON.LANGEVIN'
3676 ! include 'COMMON.LANGEVIN.lang0'
3678 ! include 'COMMON.CHAIN'
3679 ! include 'COMMON.DERIV'
3680 ! include 'COMMON.GEO'
3681 ! include 'COMMON.LOCAL'
3682 ! include 'COMMON.INTERACT'
3683 ! include 'COMMON.IOUNITS'
3684 ! include 'COMMON.NAMES'
3685 !el real(kind=8),dimension(6*nres) :: stochforcvec,stochforcvecV !(MAXRES6) maxres6=6*maxres
3686 real(kind=8),dimension(6*nres) :: stochforcvecV !(MAXRES6) maxres6=6*maxres
3687 !el common /stochcalc/ stochforcvec
3688 real(kind=8) :: ddt1,ddt2
3689 integer :: i,j,ind,inres
3691 ! Compute the stochastic forces which contribute to velocity change
3693 call stochastic_force(stochforcvecV)
3700 ddt1=ddt1+vfric_mat(i,j)*d_a_work(j)
3701 ! ddt2=ddt2+vrand_mat2(i,j)*stochforcvecV(j)
3702 ddt2=ddt2+vrand_mat2(i,j)*stochforcvec(j)
3704 d_t_work(i)=d_t_work_new(i)+0.5d0*ddt1+ddt2
3708 d_t(j,0)=d_t_work(j)
3713 d_t(j,i)=d_t_work(ind+j)
3719 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
3721 ! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
3724 d_t(j,inres)=d_t_work(ind+j)
3730 end subroutine sd_verlet2_ciccotti
3732 !-----------------------------------------------------------------------------
3734 !-----------------------------------------------------------------------------
3735 subroutine inertia_tensor
3737 ! Calculating the intertia tensor for the entire protein in order to
3738 ! remove the perpendicular components of velocity matrix which cause
3739 ! the molecule to rotate.
3742 ! implicit real*8 (a-h,o-z)
3743 ! include 'DIMENSIONS'
3744 ! include 'COMMON.CONTROL'
3745 ! include 'COMMON.VAR'
3746 ! include 'COMMON.MD'
3747 ! include 'COMMON.CHAIN'
3748 ! include 'COMMON.DERIV'
3749 ! include 'COMMON.GEO'
3750 ! include 'COMMON.LOCAL'
3751 ! include 'COMMON.INTERACT'
3752 ! include 'COMMON.IOUNITS'
3753 ! include 'COMMON.NAMES'
3755 real(kind=8),dimension(3,3) :: Im,Imcp,eigvec,Id
3756 real(kind=8),dimension(3) :: pr,eigval,L,vp,vrot
3757 real(kind=8) :: M_SC,mag,mag2,M_PEP
3758 real(kind=8),dimension(3,0:nres) :: vpp !(3,0:MAXRES)
3759 real(kind=8),dimension(3) :: vs_p,pp,incr,v
3760 real(kind=8),dimension(3,3) :: pr1,pr2
3762 !el common /gucio/ cm
3763 integer :: iti,inres,i,j,k,mnum
3774 ! calculating the center of the mass of the protein
3778 if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
3779 if (itype(i,mnum).eq.ntyp1_molec(mnum)) cycle
3780 M_PEP=M_PEP+mp(mnum)
3782 cm(j)=cm(j)+(c(j,i)+0.5d0*dc(j,i))*mp(mnum)
3791 if (mnum.eq.5) cycle
3792 iti=iabs(itype(i,mnum))
3793 M_SC=M_SC+msc(iabs(iti),mnum)
3796 cm(j)=cm(j)+msc(iabs(iti),mnum)*c(j,inres)
3800 cm(j)=cm(j)/(M_SC+M_PEP)
3805 if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
3807 pr(j)=c(j,i)+0.5d0*dc(j,i)-cm(j)
3809 Im(1,1)=Im(1,1)+mp(mnum)*(pr(2)*pr(2)+pr(3)*pr(3))
3810 Im(1,2)=Im(1,2)-mp(mnum)*pr(1)*pr(2)
3811 Im(1,3)=Im(1,3)-mp(mnum)*pr(1)*pr(3)
3812 Im(2,3)=Im(2,3)-mp(mnum)*pr(2)*pr(3)
3813 Im(2,2)=Im(2,2)+mp(mnum)*(pr(3)*pr(3)+pr(1)*pr(1))
3814 Im(3,3)=Im(3,3)+mp(mnum)*(pr(1)*pr(1)+pr(2)*pr(2))
3819 iti=iabs(itype(i,mnum))
3820 if (mnum.eq.5) cycle
3823 pr(j)=c(j,inres)-cm(j)
3825 Im(1,1)=Im(1,1)+msc(iabs(iti),mnum)*(pr(2)*pr(2)+pr(3)*pr(3))
3826 Im(1,2)=Im(1,2)-msc(iabs(iti),mnum)*pr(1)*pr(2)
3827 Im(1,3)=Im(1,3)-msc(iabs(iti),mnum)*pr(1)*pr(3)
3828 Im(2,3)=Im(2,3)-msc(iabs(iti),mnum)*pr(2)*pr(3)
3829 Im(2,2)=Im(2,2)+msc(iabs(iti),mnum)*(pr(3)*pr(3)+pr(1)*pr(1))
3830 Im(3,3)=Im(3,3)+msc(iabs(iti),mnum)*(pr(1)*pr(1)+pr(2)*pr(2))
3835 Im(1,1)=Im(1,1)+Ip(mnum)*(1-dc_norm(1,i)*dc_norm(1,i))* &
3836 vbld(i+1)*vbld(i+1)*0.25d0
3837 Im(1,2)=Im(1,2)+Ip(mnum)*(-dc_norm(1,i)*dc_norm(2,i))* &
3838 vbld(i+1)*vbld(i+1)*0.25d0
3839 Im(1,3)=Im(1,3)+Ip(mnum)*(-dc_norm(1,i)*dc_norm(3,i))* &
3840 vbld(i+1)*vbld(i+1)*0.25d0
3841 Im(2,3)=Im(2,3)+Ip(mnum)*(-dc_norm(2,i)*dc_norm(3,i))* &
3842 vbld(i+1)*vbld(i+1)*0.25d0
3843 Im(2,2)=Im(2,2)+Ip(mnum)*(1-dc_norm(2,i)*dc_norm(2,i))* &
3844 vbld(i+1)*vbld(i+1)*0.25d0
3845 Im(3,3)=Im(3,3)+Ip(mnum)*(1-dc_norm(3,i)*dc_norm(3,i))* &
3846 vbld(i+1)*vbld(i+1)*0.25d0
3852 ! if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)) then
3853 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
3854 .and.(mnum.ne.5)) then
3855 iti=iabs(itype(i,mnum))
3857 Im(1,1)=Im(1,1)+Isc(iti,mnum)*(1-dc_norm(1,inres)* &
3858 dc_norm(1,inres))*vbld(inres)*vbld(inres)
3859 Im(1,2)=Im(1,2)-Isc(iti,mnum)*(dc_norm(1,inres)* &
3860 dc_norm(2,inres))*vbld(inres)*vbld(inres)
3861 Im(1,3)=Im(1,3)-Isc(iti,mnum)*(dc_norm(1,inres)* &
3862 dc_norm(3,inres))*vbld(inres)*vbld(inres)
3863 Im(2,3)=Im(2,3)-Isc(iti,mnum)*(dc_norm(2,inres)* &
3864 dc_norm(3,inres))*vbld(inres)*vbld(inres)
3865 Im(2,2)=Im(2,2)+Isc(iti,mnum)*(1-dc_norm(2,inres)* &
3866 dc_norm(2,inres))*vbld(inres)*vbld(inres)
3867 Im(3,3)=Im(3,3)+Isc(iti,mnum)*(1-dc_norm(3,inres)* &
3868 dc_norm(3,inres))*vbld(inres)*vbld(inres)
3873 ! write(iout,*) "The angular momentum before adjustment:"
3874 ! write(iout,*) (L(j),j=1,3)
3880 ! Copying the Im matrix for the djacob subroutine
3888 ! Finding the eigenvectors and eignvalues of the inertia tensor
3889 call djacob(3,3,10000,1.0d-10,Imcp,eigvec,eigval)
3890 ! write (iout,*) "Eigenvalues & Eigenvectors"
3891 ! write (iout,'(5x,3f10.5)') (eigval(i),i=1,3)
3894 ! write (iout,'(i5,3f10.5)') i,(eigvec(i,j),j=1,3)
3896 ! Constructing the diagonalized matrix
3898 if (dabs(eigval(i)).gt.1.0d-15) then
3899 Id(i,i)=1.0d0/eigval(i)
3906 Imcp(i,j)=eigvec(j,i)
3912 pr1(i,j)=pr1(i,j)+Id(i,k)*Imcp(k,j)
3919 pr2(i,j)=pr2(i,j)+eigvec(i,k)*pr1(k,j)
3923 ! Calculating the total rotational velocity of the molecule
3926 vrot(i)=vrot(i)+pr2(i,j)*L(j)
3929 ! Resetting the velocities
3931 call vecpr(vrot(1),dc(1,i),vp)
3933 d_t(j,i)=d_t(j,i)-vp(j)
3938 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
3939 .and.(mnum.ne.5)) then
3940 ! if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)) then
3941 ! if(itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
3943 call vecpr(vrot(1),dc(1,inres),vp)
3945 d_t(j,inres)=d_t(j,inres)-vp(j)
3950 ! write(iout,*) "The angular momentum after adjustment:"
3951 ! write(iout,*) (L(j),j=1,3)
3954 end subroutine inertia_tensor
3955 !-----------------------------------------------------------------------------
3956 subroutine angmom(cm,L)
3959 ! implicit real*8 (a-h,o-z)
3960 ! include 'DIMENSIONS'
3961 ! include 'COMMON.CONTROL'
3962 ! include 'COMMON.VAR'
3963 ! include 'COMMON.MD'
3964 ! include 'COMMON.CHAIN'
3965 ! include 'COMMON.DERIV'
3966 ! include 'COMMON.GEO'
3967 ! include 'COMMON.LOCAL'
3968 ! include 'COMMON.INTERACT'
3969 ! include 'COMMON.IOUNITS'
3970 ! include 'COMMON.NAMES'
3971 real(kind=8) :: mscab
3972 real(kind=8),dimension(3) :: L,cm,pr,vp,vrot,incr,v,pp
3973 integer :: iti,inres,i,j,mnum
3974 ! Calculate the angular momentum
3983 if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
3985 pr(j)=c(j,i)+0.5d0*dc(j,i)-cm(j)
3988 v(j)=incr(j)+0.5d0*d_t(j,i)
3991 incr(j)=incr(j)+d_t(j,i)
3993 call vecpr(pr(1),v(1),vp)
3995 L(j)=L(j)+mp(mnum)*vp(j)
3999 pp(j)=0.5d0*d_t(j,i)
4001 call vecpr(pr(1),pp(1),vp)
4003 L(j)=L(j)+Ip(mnum)*vp(j)
4011 iti=iabs(itype(i,mnum))
4019 pr(j)=c(j,inres)-cm(j)
4021 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4022 .and.(mnum.ne.5)) then
4024 v(j)=incr(j)+d_t(j,inres)
4031 call vecpr(pr(1),v(1),vp)
4032 ! write (iout,*) "i",i," iti",iti," pr",(pr(j),j=1,3),&
4033 ! " v",(v(j),j=1,3)," vp",(vp(j),j=1,3)
4035 L(j)=L(j)+mscab*vp(j)
4037 ! write (iout,*) "L",(l(j),j=1,3)
4038 if (itype(i,mnum).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4039 .and.(mnum.ne.5)) then
4041 v(j)=incr(j)+d_t(j,inres)
4043 call vecpr(dc(1,inres),d_t(1,inres),vp)
4045 L(j)=L(j)+Isc(iti,mnum)*vp(j)
4049 incr(j)=incr(j)+d_t(j,i)
4053 end subroutine angmom
4054 !-----------------------------------------------------------------------------
4055 subroutine vcm_vel(vcm)
4058 ! implicit real*8 (a-h,o-z)
4059 ! include 'DIMENSIONS'
4060 ! include 'COMMON.VAR'
4061 ! include 'COMMON.MD'
4062 ! include 'COMMON.CHAIN'
4063 ! include 'COMMON.DERIV'
4064 ! include 'COMMON.GEO'
4065 ! include 'COMMON.LOCAL'
4066 ! include 'COMMON.INTERACT'
4067 ! include 'COMMON.IOUNITS'
4068 real(kind=8),dimension(3) :: vcm,vv
4069 real(kind=8) :: summas,amas
4079 if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
4081 summas=summas+mp(mnum)
4083 vcm(j)=vcm(j)+mp(mnum)*(vv(j)+0.5d0*d_t(j,i))
4087 amas=msc(iabs(itype(i,mnum)),mnum)
4092 if (itype(i,mnum).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4093 .and.(mnum.ne.5)) then
4095 vcm(j)=vcm(j)+amas*(vv(j)+d_t(j,i+nres))
4099 vcm(j)=vcm(j)+amas*vv(j)
4103 vv(j)=vv(j)+d_t(j,i)
4106 ! write (iout,*) "vcm",(vcm(j),j=1,3)," summas",summas
4108 vcm(j)=vcm(j)/summas
4111 end subroutine vcm_vel
4112 !-----------------------------------------------------------------------------
4114 !-----------------------------------------------------------------------------
4116 ! RATTLE algorithm for velocity Verlet - step 1, UNRES
4120 ! implicit real*8 (a-h,o-z)
4121 ! include 'DIMENSIONS'
4123 ! include 'COMMON.CONTROL'
4124 ! include 'COMMON.VAR'
4125 ! include 'COMMON.MD'
4127 ! include 'COMMON.LANGEVIN'
4129 ! include 'COMMON.LANGEVIN.lang0'
4131 ! include 'COMMON.CHAIN'
4132 ! include 'COMMON.DERIV'
4133 ! include 'COMMON.GEO'
4134 ! include 'COMMON.LOCAL'
4135 ! include 'COMMON.INTERACT'
4136 ! include 'COMMON.IOUNITS'
4137 ! include 'COMMON.NAMES'
4138 ! include 'COMMON.TIME1'
4139 !el real(kind=8) :: gginv(2*nres,2*nres),&
4140 !el gdc(3,2*nres,2*nres)
4141 real(kind=8) :: dC_uncor(3,2*nres) !,&
4142 !el real(kind=8) :: Cmat(2*nres,2*nres)
4143 real(kind=8) :: x(2*nres),xcorr(3,2*nres) !maxres2=2*maxres
4144 !el common /przechowalnia/ GGinv,gdc,Cmat,nbond
4145 !el common /przechowalnia/ nbond
4146 integer :: max_rattle = 5
4147 logical :: lprn = .false., lprn1 = .false., not_done
4148 real(kind=8) :: tol_rattle = 1.0d-5
4150 integer :: ii,i,j,jj,l,ind,ind1,nres2
4153 !el /common/ przechowalnia
4155 if(.not.allocated(GGinv)) allocate(GGinv(nres2,nres2))
4156 if(.not.allocated(gdc)) allocate(gdc(3,nres2,nres2))
4157 if(.not.allocated(Cmat)) allocate(Cmat(nres2,nres2))
4159 if (lprn) write (iout,*) "RATTLE1"
4163 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4164 .and.(mnum.ne.5)) nbond=nbond+1
4166 ! Make a folded form of the Ginv-matrix
4179 if (j.eq.1 .and. l.eq.1) GGinv(ii,jj)=Ginv(ind,ind1)
4184 if (itype(k,1).ne.10 .and. itype(k,mnum).ne.ntyp1_molec(mnum)&
4185 .and.(mnum.ne.5)) then
4189 if (j.eq.1 .and. l.eq.1) GGinv(ii,jj)=Ginv(ind,ind1)
4197 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4208 if (j.eq.1 .and. l.eq.1) GGinv(ii,jj)=Ginv(ind,ind1)
4212 if (itype(k,1).ne.10) then
4216 if (j.eq.1 .and. l.eq.1) GGinv(ii,jj)=Ginv(ind,ind1)
4224 write (iout,*) "Matrix GGinv"
4225 call MATOUT(nbond,nbond,MAXRES2,MAXRES2,GGinv)
4231 if (iter.gt.max_rattle) then
4232 write (iout,*) "Error - too many iterations in RATTLE."
4235 ! Calculate the matrix C = GG**(-1) dC_old o dC
4240 dC_uncor(j,ind1)=dC(j,i)
4244 if (itype(i,1).ne.10) then
4247 dC_uncor(j,ind1)=dC(j,i+nres)
4256 gdc(j,i,ind)=GGinv(i,ind)*dC_old(j,k)
4260 if (itype(k,1).ne.10) then
4263 gdc(j,i,ind)=GGinv(i,ind)*dC_old(j,k+nres)
4268 ! Calculate deviations from standard virtual-bond lengths
4272 x(ind)=vbld(i+1)**2-vbl**2
4275 if (itype(i,1).ne.10) then
4277 x(ind)=vbld(i+nres)**2-vbldsc0(1,itype(i,1))**2
4281 write (iout,*) "Coordinates and violations"
4283 write(iout,'(i5,3f10.5,5x,e15.5)') &
4284 i,(dC_uncor(j,i),j=1,3),x(i)
4286 write (iout,*) "Velocities and violations"
4290 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4291 i,ind,(d_t_new(j,i),j=1,3),scalar(d_t_new(1,i),dC_old(1,i))
4295 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4296 .and.(mnum.ne.5)) then
4299 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4300 i+nres,ind,(d_t_new(j,i+nres),j=1,3),&
4301 scalar(d_t_new(1,i+nres),dC_old(1,i+nres))
4304 ! write (iout,*) "gdc"
4306 ! write (iout,*) "i",i
4308 ! write (iout,'(i5,3f10.5)') j,(gdc(k,j,i),k=1,3)
4314 if (dabs(x(i)).gt.xmax) then
4318 if (xmax.lt.tol_rattle) then
4322 ! Calculate the matrix of the system of equations
4327 Cmat(i,j)=Cmat(i,j)+dC_uncor(k,i)*gdc(k,i,j)
4332 write (iout,*) "Matrix Cmat"
4333 call MATOUT(nbond,nbond,MAXRES2,MAXRES2,Cmat)
4335 call gauss(Cmat,X,MAXRES2,nbond,1,*10)
4336 ! Add constraint term to positions
4343 xx = xx+x(ii)*gdc(j,ind,ii)
4347 d_t_new(j,i)=d_t_new(j,i)-xx/d_time
4351 if (itype(i,1).ne.10) then
4356 xx = xx+x(ii)*gdc(j,ind,ii)
4359 dC(j,i+nres)=dC(j,i+nres)-xx
4360 d_t_new(j,i+nres)=d_t_new(j,i+nres)-xx/d_time
4364 ! Rebuild the chain using the new coordinates
4365 call chainbuild_cart
4367 write (iout,*) "New coordinates, Lagrange multipliers,",&
4368 " and differences between actual and standard bond lengths"
4372 xx=vbld(i+1)**2-vbl**2
4373 write (iout,'(i5,3f10.5,5x,f10.5,e15.5)') &
4374 i,(dC(j,i),j=1,3),x(ind),xx
4378 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4381 xx=vbld(i+nres)**2-vbldsc0(1,itype(i,1))**2
4382 write (iout,'(i5,3f10.5,5x,f10.5,e15.5)') &
4383 i,(dC(j,i+nres),j=1,3),x(ind),xx
4386 write (iout,*) "Velocities and violations"
4390 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4391 i,ind,(d_t_new(j,i),j=1,3),scalar(d_t_new(1,i),dC_old(1,i))
4394 if (itype(i,1).ne.10) then
4396 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4397 i+nres,ind,(d_t_new(j,i+nres),j=1,3),&
4398 scalar(d_t_new(1,i+nres),dC_old(1,i+nres))
4405 10 write (iout,*) "Error - singularity in solving the system",&
4406 " of equations for Lagrange multipliers."
4410 "RATTLE inactive; use -DRATTLE switch at compile time."
4413 end subroutine rattle1
4414 !-----------------------------------------------------------------------------
4416 ! RATTLE algorithm for velocity Verlet - step 2, UNRES
4420 ! implicit real*8 (a-h,o-z)
4421 ! include 'DIMENSIONS'
4423 ! include 'COMMON.CONTROL'
4424 ! include 'COMMON.VAR'
4425 ! include 'COMMON.MD'
4427 ! include 'COMMON.LANGEVIN'
4429 ! include 'COMMON.LANGEVIN.lang0'
4431 ! include 'COMMON.CHAIN'
4432 ! include 'COMMON.DERIV'
4433 ! include 'COMMON.GEO'
4434 ! include 'COMMON.LOCAL'
4435 ! include 'COMMON.INTERACT'
4436 ! include 'COMMON.IOUNITS'
4437 ! include 'COMMON.NAMES'
4438 ! include 'COMMON.TIME1'
4439 !el real(kind=8) :: gginv(2*nres,2*nres),&
4440 !el gdc(3,2*nres,2*nres)
4441 real(kind=8) :: dC_uncor(3,2*nres) !,&
4442 !el Cmat(2*nres,2*nres)
4443 real(kind=8) :: x(2*nres) !maxres2=2*maxres
4444 !el common /przechowalnia/ GGinv,gdc,Cmat,nbond
4445 !el common /przechowalnia/ nbond
4446 integer :: max_rattle = 5
4447 logical :: lprn = .false., lprn1 = .false., not_done
4448 real(kind=8) :: tol_rattle = 1.0d-5
4452 !el /common/ przechowalnia
4453 if(.not.allocated(GGinv)) allocate(GGinv(nres2,nres2))
4454 if(.not.allocated(gdc)) allocate(gdc(3,nres2,nres2))
4455 if(.not.allocated(Cmat)) allocate(Cmat(nres2,nres2))
4457 if (lprn) write (iout,*) "RATTLE2"
4458 if (lprn) write (iout,*) "Velocity correction"
4459 ! Calculate the matrix G dC
4465 gdc(j,i,ind)=GGinv(i,ind)*dC(j,k)
4470 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4471 .and.(mnum.ne.5)) then
4474 gdc(j,i,ind)=GGinv(i,ind)*dC(j,k+nres)
4480 ! write (iout,*) "gdc"
4482 ! write (iout,*) "i",i
4484 ! write (iout,'(i5,3f10.5)') j,(gdc(k,j,i),k=1,3)
4488 ! Calculate the matrix of the system of equations
4495 Cmat(ind,j)=Cmat(ind,j)+dC(k,i)*gdc(k,ind,j)
4501 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4502 .and.(mnum.ne.5)) then
4507 Cmat(ind,j)=Cmat(ind,j)+dC(k,i+nres)*gdc(k,ind,j)
4512 ! Calculate the scalar product dC o d_t_new
4516 x(ind)=scalar(d_t(1,i),dC(1,i))
4520 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4521 .and.(mnum.ne.5)) then
4523 x(ind)=scalar(d_t(1,i+nres),dC(1,i+nres))
4527 write (iout,*) "Velocities and violations"
4531 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4532 i,ind,(d_t(j,i),j=1,3),x(ind)
4536 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4537 .and.(mnum.ne.5)) then
4539 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4540 i+nres,ind,(d_t(j,i+nres),j=1,3),x(ind)
4546 if (dabs(x(i)).gt.xmax) then
4550 if (xmax.lt.tol_rattle) then
4555 write (iout,*) "Matrix Cmat"
4556 call MATOUT(nbond,nbond,MAXRES2,MAXRES2,Cmat)
4558 call gauss(Cmat,X,MAXRES2,nbond,1,*10)
4559 ! Add constraint term to velocities
4566 xx = xx+x(ii)*gdc(j,ind,ii)
4568 d_t(j,i)=d_t(j,i)-xx
4573 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4574 .and.(mnum.ne.5)) then
4579 xx = xx+x(ii)*gdc(j,ind,ii)
4581 d_t(j,i+nres)=d_t(j,i+nres)-xx
4587 "New velocities, Lagrange multipliers violations"
4591 if (lprn) write (iout,'(2i5,3f10.5,5x,2e15.5)') &
4592 i,ind,(d_t(j,i),j=1,3),x(ind),scalar(d_t(1,i),dC(1,i))
4596 if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
4599 write (iout,'(2i5,3f10.5,5x,2e15.5)') &
4600 i+nres,ind,(d_t(j,i+nres),j=1,3),x(ind),&
4601 scalar(d_t(1,i+nres),dC(1,i+nres))
4607 10 write (iout,*) "Error - singularity in solving the system",&
4608 " of equations for Lagrange multipliers."
4612 "RATTLE inactive; use -DRATTLE option at compile time."
4615 end subroutine rattle2
4616 !-----------------------------------------------------------------------------
4617 subroutine rattle_brown
4618 ! RATTLE/LINCS algorithm for Brownian dynamics, UNRES
4622 ! implicit real*8 (a-h,o-z)
4623 ! include 'DIMENSIONS'
4625 ! include 'COMMON.CONTROL'
4626 ! include 'COMMON.VAR'
4627 ! include 'COMMON.MD'
4629 ! include 'COMMON.LANGEVIN'
4631 ! include 'COMMON.LANGEVIN.lang0'
4633 ! include 'COMMON.CHAIN'
4634 ! include 'COMMON.DERIV'
4635 ! include 'COMMON.GEO'
4636 ! include 'COMMON.LOCAL'
4637 ! include 'COMMON.INTERACT'
4638 ! include 'COMMON.IOUNITS'
4639 ! include 'COMMON.NAMES'
4640 ! include 'COMMON.TIME1'
4641 !el real(kind=8) :: gginv(2*nres,2*nres),&
4642 !el gdc(3,2*nres,2*nres)
4643 real(kind=8) :: dC_uncor(3,2*nres) !,&
4644 !el real(kind=8) :: Cmat(2*nres,2*nres)
4645 real(kind=8) :: x(2*nres) !maxres2=2*maxres
4646 !el common /przechowalnia/ GGinv,gdc,Cmat,nbond
4647 !el common /przechowalnia/ nbond
4648 integer :: max_rattle = 5
4649 logical :: lprn = .false., lprn1 = .false., not_done
4650 real(kind=8) :: tol_rattle = 1.0d-5
4654 !el /common/ przechowalnia
4655 if(.not.allocated(GGinv)) allocate(GGinv(nres2,nres2))
4656 if(.not.allocated(gdc)) allocate(gdc(3,nres2,nres2))
4657 if(.not.allocated(Cmat)) allocate(Cmat(nres2,nres2))
4660 if (lprn) write (iout,*) "RATTLE_BROWN"
4663 if (itype(i,1).ne.10) nbond=nbond+1
4665 ! Make a folded form of the Ginv-matrix
4678 if (j.eq.1 .and. l.eq.1) GGinv(ii,jj)=fricmat(ind,ind1)
4682 if (itype(k,1).ne.10) then
4686 if (j.eq.1 .and. l.eq.1) GGinv(ii,jj)=fricmat(ind,ind1)
4693 if (itype(i,1).ne.10) then
4703 if (j.eq.1 .and. l.eq.1) GGinv(ii,jj)=fricmat(ind,ind1)
4707 if (itype(k,1).ne.10) then
4711 if (j.eq.1 .and. l.eq.1)GGinv(ii,jj)=fricmat(ind,ind1)
4719 write (iout,*) "Matrix GGinv"
4720 call MATOUT(nbond,nbond,MAXRES2,MAXRES2,GGinv)
4726 if (iter.gt.max_rattle) then
4727 write (iout,*) "Error - too many iterations in RATTLE."
4730 ! Calculate the matrix C = GG**(-1) dC_old o dC
4735 dC_uncor(j,ind1)=dC(j,i)
4739 if (itype(i,1).ne.10) then
4742 dC_uncor(j,ind1)=dC(j,i+nres)
4751 gdc(j,i,ind)=GGinv(i,ind)*dC_old(j,k)
4755 if (itype(k,1).ne.10) then
4758 gdc(j,i,ind)=GGinv(i,ind)*dC_old(j,k+nres)
4763 ! Calculate deviations from standard virtual-bond lengths
4767 x(ind)=vbld(i+1)**2-vbl**2
4770 if (itype(i,1).ne.10) then
4772 x(ind)=vbld(i+nres)**2-vbldsc0(1,itype(i,1))**2
4776 write (iout,*) "Coordinates and violations"
4778 write(iout,'(i5,3f10.5,5x,e15.5)') &
4779 i,(dC_uncor(j,i),j=1,3),x(i)
4781 write (iout,*) "Velocities and violations"
4785 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4786 i,ind,(d_t(j,i),j=1,3),scalar(d_t(1,i),dC_old(1,i))
4789 if (itype(i,1).ne.10) then
4791 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4792 i+nres,ind,(d_t(j,i+nres),j=1,3),&
4793 scalar(d_t(1,i+nres),dC_old(1,i+nres))
4796 write (iout,*) "gdc"
4798 write (iout,*) "i",i
4800 write (iout,'(i5,3f10.5)') j,(gdc(k,j,i),k=1,3)
4806 if (dabs(x(i)).gt.xmax) then
4810 if (xmax.lt.tol_rattle) then
4814 ! Calculate the matrix of the system of equations
4819 Cmat(i,j)=Cmat(i,j)+dC_uncor(k,i)*gdc(k,i,j)
4824 write (iout,*) "Matrix Cmat"
4825 call MATOUT(nbond,nbond,MAXRES2,MAXRES2,Cmat)
4827 call gauss(Cmat,X,MAXRES2,nbond,1,*10)
4828 ! Add constraint term to positions
4835 xx = xx+x(ii)*gdc(j,ind,ii)
4838 d_t(j,i)=d_t(j,i)+xx/d_time
4843 if (itype(i,1).ne.10) then
4848 xx = xx+x(ii)*gdc(j,ind,ii)
4851 d_t(j,i+nres)=d_t(j,i+nres)+xx/d_time
4852 dC(j,i+nres)=dC(j,i+nres)+xx
4856 ! Rebuild the chain using the new coordinates
4857 call chainbuild_cart
4859 write (iout,*) "New coordinates, Lagrange multipliers,",&
4860 " and differences between actual and standard bond lengths"
4864 xx=vbld(i+1)**2-vbl**2
4865 write (iout,'(i5,3f10.5,5x,f10.5,e15.5)') &
4866 i,(dC(j,i),j=1,3),x(ind),xx
4869 if (itype(i,1).ne.10) then
4871 xx=vbld(i+nres)**2-vbldsc0(1,itype(i,1))**2
4872 write (iout,'(i5,3f10.5,5x,f10.5,e15.5)') &
4873 i,(dC(j,i+nres),j=1,3),x(ind),xx
4876 write (iout,*) "Velocities and violations"
4880 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4881 i,ind,(d_t_new(j,i),j=1,3),scalar(d_t_new(1,i),dC_old(1,i))
4884 if (itype(i,1).ne.10) then
4886 write (iout,'(2i5,3f10.5,5x,e15.5)') &
4887 i+nres,ind,(d_t_new(j,i+nres),j=1,3),&
4888 scalar(d_t_new(1,i+nres),dC_old(1,i+nres))
4895 10 write (iout,*) "Error - singularity in solving the system",&
4896 " of equations for Lagrange multipliers."
4900 "RATTLE inactive; use -DRATTLE option at compile time"
4903 end subroutine rattle_brown
4904 !-----------------------------------------------------------------------------
4906 !-----------------------------------------------------------------------------
4907 subroutine friction_force
4912 ! implicit real*8 (a-h,o-z)
4913 ! include 'DIMENSIONS'
4914 ! include 'COMMON.VAR'
4915 ! include 'COMMON.CHAIN'
4916 ! include 'COMMON.DERIV'
4917 ! include 'COMMON.GEO'
4918 ! include 'COMMON.LOCAL'
4919 ! include 'COMMON.INTERACT'
4920 ! include 'COMMON.MD'
4922 ! include 'COMMON.LANGEVIN'
4924 ! include 'COMMON.LANGEVIN.lang0'
4926 ! include 'COMMON.IOUNITS'
4927 !el real(kind=8),dimension(6*nres) :: gamvec !(MAXRES6) maxres6=6*maxres
4928 !el common /syfek/ gamvec
4929 real(kind=8) :: vv(3),vvtot(3,nres),v_work(6*nres) !,&
4930 !el ginvfric(2*nres,2*nres) !maxres2=2*maxres
4931 !el common /przechowalnia/ ginvfric
4933 logical :: lprn = .false., checkmode = .false.
4934 integer :: i,j,ind,k,nres2,nres6,mnum
4938 if(.not.allocated(gamvec)) allocate(gamvec(nres6)) !(MAXRES6)
4939 if(.not.allocated(ginvfric)) allocate(ginvfric(nres2,nres2)) !maxres2=2*maxres
4947 d_t_work(j)=d_t(j,0)
4952 d_t_work(ind+j)=d_t(j,i)
4958 if ((itype(i,1).ne.10).and.(itype(i,mnum).ne.ntyp1_molec(mnum))&
4959 .and.(mnum.ne.5)) then
4961 d_t_work(ind+j)=d_t(j,i+nres)
4967 call fricmat_mult(d_t_work,fric_work)
4969 if (.not.checkmode) return
4972 write (iout,*) "d_t_work and fric_work"
4974 write (iout,'(i3,2e15.5)') i,d_t_work(i),fric_work(i)
4978 friction(j,0)=fric_work(j)
4983 friction(j,i)=fric_work(ind+j)
4989 if ((itype(i,1).ne.10).and.(itype(i,mnum).ne.ntyp1_molec(mnum))&
4990 .and.(mnum.ne.5)) then
4991 ! if ((itype(i,1).ne.10).and.(itype(i,1).ne.ntyp1)) then
4993 friction(j,i+nres)=fric_work(ind+j)
4999 write(iout,*) "Friction backbone"
5001 write(iout,'(i5,3e15.5,5x,3e15.5)') &
5002 i,(friction(j,i),j=1,3),(d_t(j,i),j=1,3)
5004 write(iout,*) "Friction side chain"
5006 write(iout,'(i5,3e15.5,5x,3e15.5)') &
5007 i,(friction(j,i+nres),j=1,3),(d_t(j,i+nres),j=1,3)
5016 vvtot(j,i)=vv(j)+0.5d0*d_t(j,i)
5017 vvtot(j,i+nres)=vv(j)+d_t(j,i+nres)
5018 vv(j)=vv(j)+d_t(j,i)
5021 write (iout,*) "vvtot backbone and sidechain"
5023 write (iout,'(i5,3e15.5,5x,3e15.5)') i,(vvtot(j,i),j=1,3),&
5024 (vvtot(j,i+nres),j=1,3)
5029 v_work(ind+j)=vvtot(j,i)
5035 v_work(ind+j)=vvtot(j,i+nres)
5039 write (iout,*) "v_work gamvec and site-based friction forces"
5041 write (iout,'(i5,3e15.5)') i,v_work(i),gamvec(i),&
5045 ! fric_work1(i)=0.0d0
5047 ! fric_work1(i)=fric_work1(i)-A(j,i)*gamvec(j)*v_work(j)
5050 ! write (iout,*) "fric_work and fric_work1"
5052 ! write (iout,'(i5,2e15.5)') i,fric_work(i),fric_work1(i)
5058 ginvfric(i,j)=ginvfric(i,j)+ginv(i,k)*fricmat(k,j)
5062 write (iout,*) "ginvfric"
5064 write (iout,'(i5,100f8.3)') i,(ginvfric(i,j),j=1,dimen)
5066 write (iout,*) "symmetry check"
5069 write (iout,*) i,j,ginvfric(i,j)-ginvfric(j,i)
5074 end subroutine friction_force
5075 !-----------------------------------------------------------------------------
5076 subroutine setup_fricmat
5080 use control_data, only:time_Bcast
5081 use control, only:tcpu
5083 ! implicit real*8 (a-h,o-z)
5087 real(kind=8) :: time00
5089 ! include 'DIMENSIONS'
5090 ! include 'COMMON.VAR'
5091 ! include 'COMMON.CHAIN'
5092 ! include 'COMMON.DERIV'
5093 ! include 'COMMON.GEO'
5094 ! include 'COMMON.LOCAL'
5095 ! include 'COMMON.INTERACT'
5096 ! include 'COMMON.MD'
5097 ! include 'COMMON.SETUP'
5098 ! include 'COMMON.TIME1'
5099 ! integer licznik /0/
5102 ! include 'COMMON.LANGEVIN'
5104 ! include 'COMMON.LANGEVIN.lang0'
5106 ! include 'COMMON.IOUNITS'
5108 integer :: i,j,ind,ind1,m
5109 logical :: lprn = .false.
5110 real(kind=8) :: dtdi !el ,gamvec(2*nres)
5111 !el real(kind=8),dimension(2*nres,2*nres) :: ginvfric,fcopy
5112 ! real(kind=8),allocatable,dimension(:,:) :: fcopy
5113 !el real(kind=8),dimension(2*nres*(2*nres+1)/2) :: Ghalf !(mmaxres2) (mmaxres2=(maxres2*(maxres2+1)/2))
5114 !el common /syfek/ gamvec
5115 real(kind=8) :: work(8*2*nres)
5116 integer :: iwork(2*nres)
5117 !el common /przechowalnia/ ginvfric,Ghalf,fcopy
5118 integer :: ii,iti,k,l,nzero,nres2,nres6,ierr,mnum
5122 if(.not.allocated(fricmat)) allocate(fricmat(nres2,nres2))
5123 if(.not.allocated(fcopy)) allocate(fcopy(nres2,nres2)) !maxres2=2*maxres
5124 if (fg_rank.ne.king) goto 10
5129 if(.not.allocated(gamvec)) allocate(gamvec(nres2)) !(MAXRES2)
5130 if(.not.allocated(ginvfric)) allocate(ginvfric(nres2,nres2)) !maxres2=2*maxres
5131 if(.not.allocated(fcopy)) allocate(fcopy(nres2,nres2)) !maxres2=2*maxres
5132 !el allocate(fcopy(nres2,nres2)) !maxres2=2*maxres
5133 if(.not.allocated(Ghalf)) allocate(Ghalf(nres2*(nres2+1)/2)) !maxres2=2*maxres
5135 if(.not.allocated(fricmat)) allocate(fricmat(nres2,nres2))
5136 ! Zeroing out fricmat
5142 ! Load the friction coefficients corresponding to peptide groups
5147 gamvec(ind1)=gamp(mnum)
5149 ! Load the friction coefficients corresponding to side chains
5153 gamsc(ntyp1_molec(j),j)=1.0d0
5160 gamvec(ii)=gamsc(iabs(iti),mnum)
5162 if (surfarea) call sdarea(gamvec)
5164 ! write (iout,*) "Matrix A and vector gamma"
5166 ! write (iout,'(i2,$)') i
5168 ! write (iout,'(f4.1,$)') A(i,j)
5170 ! write (iout,'(f8.3)') gamvec(i)
5174 write (iout,*) "Vector gamvec"
5176 write (iout,'(i5,f10.5)') i, gamvec(i)
5180 ! The friction matrix
5185 dtdi=dtdi+A(j,k)*A(j,i)*gamvec(j)
5192 write (iout,'(//a)') "Matrix fricmat"
5193 call matout2(dimen,dimen,nres2,nres2,fricmat)
5195 if (lang.eq.2 .or. lang.eq.3) then
5196 ! Mass-scale the friction matrix if non-direct integration will be performed
5202 Ginvfric(i,j)=Ginvfric(i,j)+ &
5203 Gsqrm(i,k)*Gsqrm(l,j)*fricmat(k,l)
5208 ! Diagonalize the friction matrix
5213 Ghalf(ind)=Ginvfric(i,j)
5216 call gldiag(nres2,dimen,dimen,Ghalf,work,fricgam,fricvec,&
5219 write (iout,'(//2a)') "Eigenvectors and eigenvalues of the",&
5220 " mass-scaled friction matrix"
5221 call eigout(dimen,dimen,nres2,nres2,fricvec,fricgam)
5223 ! Precompute matrices for tinker stochastic integrator
5230 mt1(i,j)=mt1(i,j)+fricvec(k,i)*gsqrm(k,j)
5231 mt2(i,j)=mt2(i,j)+fricvec(k,i)*gsqrp(k,j)
5237 else if (lang.eq.4) then
5238 ! Diagonalize the friction matrix
5243 Ghalf(ind)=fricmat(i,j)
5246 call gldiag(nres2,dimen,dimen,Ghalf,work,fricgam,fricvec,&
5249 write (iout,'(//2a)') "Eigenvectors and eigenvalues of the",&
5251 call eigout(dimen,dimen,nres2,nres2,fricvec,fricgam)
5253 ! Determine the number of zero eigenvalues of the friction matrix
5254 nzero=max0(dimen-dimen1,0)
5255 ! do while (fricgam(nzero+1).le.1.0d-5 .and. nzero.lt.dimen)
5258 write (iout,*) "Number of zero eigenvalues:",nzero
5263 fricmat(i,j)=fricmat(i,j) &
5264 +fricvec(i,k)*fricvec(j,k)/fricgam(k)
5269 write (iout,'(//a)') "Generalized inverse of fricmat"
5270 call matout(dimen,dimen,nres6,nres6,fricmat)
5275 if (nfgtasks.gt.1) then
5276 if (fg_rank.eq.0) then
5277 ! The matching BROADCAST for fg processors is called in ERGASTULUM
5283 call MPI_Bcast(10,1,MPI_INTEGER,king,FG_COMM,IERROR)
5285 time_Bcast=time_Bcast+MPI_Wtime()-time00
5287 time_Bcast=time_Bcast+tcpu()-time00
5289 ! print *,"Processor",myrank,
5290 ! & " BROADCAST iorder in SETUP_FRICMAT"
5293 write (iout,*) "setup_fricmat licznik"!,licznik !sp
5299 ! Scatter the friction matrix
5300 call MPI_Scatterv(fricmat(1,1),nginv_counts(0),&
5301 nginv_start(0),MPI_DOUBLE_PRECISION,fcopy(1,1),&
5302 myginv_ng_count,MPI_DOUBLE_PRECISION,king,FG_COMM,IERROR)
5305 time_scatter=time_scatter+MPI_Wtime()-time00
5306 time_scatter_fmat=time_scatter_fmat+MPI_Wtime()-time00
5308 time_scatter=time_scatter+tcpu()-time00
5309 time_scatter_fmat=time_scatter_fmat+tcpu()-time00
5313 do j=1,2*my_ng_count
5314 fricmat(j,i)=fcopy(i,j)
5317 ! write (iout,*) "My chunk of fricmat"
5318 ! call MATOUT2(my_ng_count,dimen,maxres2,maxres2,fcopy)
5322 end subroutine setup_fricmat
5323 !-----------------------------------------------------------------------------
5324 subroutine stochastic_force(stochforcvec)
5327 use random, only:anorm_distr
5328 ! implicit real*8 (a-h,o-z)
5329 ! include 'DIMENSIONS'
5330 use control, only: tcpu
5335 ! include 'COMMON.VAR'
5336 ! include 'COMMON.CHAIN'
5337 ! include 'COMMON.DERIV'
5338 ! include 'COMMON.GEO'
5339 ! include 'COMMON.LOCAL'
5340 ! include 'COMMON.INTERACT'
5341 ! include 'COMMON.MD'
5342 ! include 'COMMON.TIME1'
5344 ! include 'COMMON.LANGEVIN'
5346 ! include 'COMMON.LANGEVIN.lang0'
5348 ! include 'COMMON.IOUNITS'
5350 real(kind=8) :: x,sig,lowb,highb
5351 real(kind=8) :: ff(3),force(3,0:2*nres),zeta2,lowb2
5352 real(kind=8) :: highb2,sig2,forcvec(6*nres),stochforcvec(6*nres)
5353 real(kind=8) :: time00
5354 logical :: lprn = .false.
5355 integer :: i,j,ind,mnum
5359 stochforc(j,i)=0.0d0
5369 ! Compute the stochastic forces acting on bodies. Store in force.
5375 force(j,i)=anorm_distr(x,sig,lowb,highb)
5383 force(j,i+nres)=anorm_distr(x,sig2,lowb2,highb2)
5387 time_fsample=time_fsample+MPI_Wtime()-time00
5389 time_fsample=time_fsample+tcpu()-time00
5391 ! Compute the stochastic forces acting on virtual-bond vectors.
5397 stochforc(j,i)=ff(j)+0.5d0*force(j,i)
5400 ff(j)=ff(j)+force(j,i)
5402 ! if (itype(i+1,1).ne.ntyp1) then
5404 if (itype(i+1,mnum).ne.ntyp1_molec(mnum)) then
5406 stochforc(j,i)=stochforc(j,i)+force(j,i+nres+1)
5407 ff(j)=ff(j)+force(j,i+nres+1)
5412 stochforc(j,0)=ff(j)+force(j,nnt+nres)
5416 if ((itype(i,1).ne.10).and.(itype(i,mnum).ne.ntyp1_molec(mnum))&
5417 .and.(mnum.ne.5)) then
5418 ! if ((itype(i,1).ne.10).and.(itype(i,1).ne.ntyp1)) then
5420 stochforc(j,i+nres)=force(j,i+nres)
5426 stochforcvec(j)=stochforc(j,0)
5431 stochforcvec(ind+j)=stochforc(j,i)
5437 if ((itype(i,1).ne.10).and.(itype(i,mnum).ne.ntyp1_molec(mnum))&
5438 .and.(mnum.ne.5)) then
5439 ! if ((itype(i,1).ne.10).and.(itype(i,1).ne.ntyp1)) then
5441 stochforcvec(ind+j)=stochforc(j,i+nres)
5447 write (iout,*) "stochforcvec"
5449 write(iout,'(i5,e15.5)') i,stochforcvec(i)
5451 write(iout,*) "Stochastic forces backbone"
5453 write(iout,'(i5,3e15.5)') i,(stochforc(j,i),j=1,3)
5455 write(iout,*) "Stochastic forces side chain"
5457 write(iout,'(i5,3e15.5)') &
5458 i,(stochforc(j,i+nres),j=1,3)
5466 write (iout,*) i,ind
5468 forcvec(ind+j)=force(j,i)
5473 write (iout,*) i,ind
5475 forcvec(j+ind)=force(j,i+nres)
5480 write (iout,*) "forcvec"
5484 write (iout,'(2i3,2f10.5)') i,j,force(j,i),&
5491 write (iout,'(2i3,2f10.5)') i,j,force(j,i+nres),&
5500 end subroutine stochastic_force
5501 !-----------------------------------------------------------------------------
5502 subroutine sdarea(gamvec)
5504 ! Scale the friction coefficients according to solvent accessible surface areas
5505 ! Code adapted from TINKER
5509 ! implicit real*8 (a-h,o-z)
5510 ! include 'DIMENSIONS'
5511 ! include 'COMMON.CONTROL'
5512 ! include 'COMMON.VAR'
5513 ! include 'COMMON.MD'
5515 ! include 'COMMON.LANGEVIN'
5517 ! include 'COMMON.LANGEVIN.lang0'
5519 ! include 'COMMON.CHAIN'
5520 ! include 'COMMON.DERIV'
5521 ! include 'COMMON.GEO'
5522 ! include 'COMMON.LOCAL'
5523 ! include 'COMMON.INTERACT'
5524 ! include 'COMMON.IOUNITS'
5525 ! include 'COMMON.NAMES'
5526 real(kind=8),dimension(2*nres) :: radius,gamvec !(maxres2)
5527 real(kind=8),parameter :: twosix = 1.122462048309372981d0
5528 logical :: lprn = .false.
5529 real(kind=8) :: probe,area,ratio
5530 integer :: i,j,ind,iti,mnum
5532 ! determine new friction coefficients every few SD steps
5534 ! set the atomic radii to estimates of sigma values
5536 ! print *,"Entered sdarea"
5542 ! Load peptide group radii
5545 radius(i)=pstok(mnum)
5547 ! Load side chain radii
5551 radius(i+nres)=restok(iti,mnum)
5554 ! write (iout,*) "i",i," radius",radius(i)
5557 radius(i) = radius(i) / twosix
5558 if (radius(i) .ne. 0.0d0) radius(i) = radius(i) + probe
5561 ! scale atomic friction coefficients by accessible area
5563 if (lprn) write (iout,*) &
5564 "Original gammas, surface areas, scaling factors, new gammas, ",&
5565 "std's of stochastic forces"
5568 if (radius(i).gt.0.0d0) then
5569 call surfatom (i,area,radius)
5570 ratio = dmax1(area/(4.0d0*pi*radius(i)**2),1.0d-1)
5571 if (lprn) write (iout,'(i5,3f10.5,$)') &
5572 i,gamvec(ind+1),area,ratio
5575 gamvec(ind) = ratio * gamvec(ind)
5578 stdforcp(i)=stdfp(mnum)*dsqrt(gamvec(ind))
5579 if (lprn) write (iout,'(2f10.5)') gamvec(ind),stdforcp(i)
5583 if (radius(i+nres).gt.0.0d0) then
5584 call surfatom (i+nres,area,radius)
5585 ratio = dmax1(area/(4.0d0*pi*radius(i+nres)**2),1.0d-1)
5586 if (lprn) write (iout,'(i5,3f10.5,$)') &
5587 i,gamvec(ind+1),area,ratio
5590 gamvec(ind) = ratio * gamvec(ind)
5593 stdforcsc(i)=stdfsc(itype(i,mnum),mnum)*dsqrt(gamvec(ind))
5594 if (lprn) write (iout,'(2f10.5)') gamvec(ind),stdforcsc(i)
5599 end subroutine sdarea
5600 !-----------------------------------------------------------------------------
5602 !-----------------------------------------------------------------------------
5605 ! ###################################################
5606 ! ## COPYRIGHT (C) 1996 by Jay William Ponder ##
5607 ! ## All Rights Reserved ##
5608 ! ###################################################
5610 ! ################################################################
5612 ! ## subroutine surfatom -- exposed surface area of an atom ##
5614 ! ################################################################
5617 ! "surfatom" performs an analytical computation of the surface
5618 ! area of a specified atom; a simplified version of "surface"
5620 ! literature references:
5622 ! T. J. Richmond, "Solvent Accessible Surface Area and
5623 ! Excluded Volume in Proteins", Journal of Molecular Biology,
5626 ! L. Wesson and D. Eisenberg, "Atomic Solvation Parameters
5627 ! Applied to Molecular Dynamics of Proteins in Solution",
5628 ! Protein Science, 1, 227-235 (1992)
5630 ! variables and parameters:
5632 ! ir number of atom for which area is desired
5633 ! area accessible surface area of the atom
5634 ! radius radii of each of the individual atoms
5637 subroutine surfatom(ir,area,radius)
5639 ! implicit real*8 (a-h,o-z)
5640 ! include 'DIMENSIONS'
5642 ! include 'COMMON.GEO'
5643 ! include 'COMMON.IOUNITS'
5645 integer :: nsup,nstart_sup
5646 ! double precision c,dc,dc_old,d_c_work,xloc,xrot,dc_norm
5647 ! common /chain/ c(3,maxres2+2),dc(3,0:maxres2),dc_old(3,0:maxres2),
5648 ! & xloc(3,maxres),xrot(3,maxres),dc_norm(3,0:maxres2),
5649 ! & dc_work(MAXRES6),nres,nres0
5650 integer,parameter :: maxarc=300
5654 integer :: mi,ni,narc
5655 integer :: key(maxarc)
5656 integer :: intag(maxarc)
5657 integer :: intag1(maxarc)
5658 real(kind=8) :: area,arcsum
5659 real(kind=8) :: arclen,exang
5660 real(kind=8) :: delta,delta2
5661 real(kind=8) :: eps,rmove
5662 real(kind=8) :: xr,yr,zr
5663 real(kind=8) :: rr,rrsq
5664 real(kind=8) :: rplus,rminus
5665 real(kind=8) :: axx,axy,axz
5666 real(kind=8) :: ayx,ayy
5667 real(kind=8) :: azx,azy,azz
5668 real(kind=8) :: uxj,uyj,uzj
5669 real(kind=8) :: tx,ty,tz
5670 real(kind=8) :: txb,tyb,td
5671 real(kind=8) :: tr2,tr,txr,tyr
5672 real(kind=8) :: tk1,tk2
5673 real(kind=8) :: thec,the,t,tb
5674 real(kind=8) :: txk,tyk,tzk
5675 real(kind=8) :: t1,ti,tf,tt
5676 real(kind=8) :: txj,tyj,tzj
5677 real(kind=8) :: ccsq,cc,xysq
5678 real(kind=8) :: bsqk,bk,cosine
5679 real(kind=8) :: dsqj,gi,pix2
5680 real(kind=8) :: therk,dk,gk
5681 real(kind=8) :: risqk,rik
5682 real(kind=8) :: radius(2*nres) !(maxatm) (maxatm=maxres2)
5683 real(kind=8) :: ri(maxarc),risq(maxarc)
5684 real(kind=8) :: ux(maxarc),uy(maxarc),uz(maxarc)
5685 real(kind=8) :: xc(maxarc),yc(maxarc),zc(maxarc)
5686 real(kind=8) :: xc1(maxarc),yc1(maxarc),zc1(maxarc)
5687 real(kind=8) :: dsq(maxarc),bsq(maxarc)
5688 real(kind=8) :: dsq1(maxarc),bsq1(maxarc)
5689 real(kind=8) :: arci(maxarc),arcf(maxarc)
5690 real(kind=8) :: ex(maxarc),lt(maxarc),gr(maxarc)
5691 real(kind=8) :: b(maxarc),b1(maxarc),bg(maxarc)
5692 real(kind=8) :: kent(maxarc),kout(maxarc)
5693 real(kind=8) :: ther(maxarc)
5694 logical :: moved,top
5695 logical :: omit(maxarc)
5698 ! maxatm = 2*nres !maxres2 maxres2=2*maxres
5699 ! maxlight = 8*maxatm
5702 ! maxtors = 4*maxatm
5704 ! zero out the surface area for the sphere of interest
5707 ! write (2,*) "ir",ir," radius",radius(ir)
5708 if (radius(ir) .eq. 0.0d0) return
5710 ! set the overlap significance and connectivity shift
5714 delta2 = delta * delta
5719 ! store coordinates and radius of the sphere of interest
5727 ! initialize values of some counters and summations
5736 ! test each sphere to see if it overlaps the sphere of interest
5739 if (i.eq.ir .or. radius(i).eq.0.0d0) goto 30
5740 rplus = rr + radius(i)
5742 if (abs(tx) .ge. rplus) goto 30
5744 if (abs(ty) .ge. rplus) goto 30
5746 if (abs(tz) .ge. rplus) goto 30
5748 ! check for sphere overlap by testing distance against radii
5750 xysq = tx*tx + ty*ty
5751 if (xysq .lt. delta2) then
5758 if (rplus-cc .le. delta) goto 30
5759 rminus = rr - radius(i)
5761 ! check to see if sphere of interest is completely buried
5763 if (cc-abs(rminus) .le. delta) then
5764 if (rminus .le. 0.0d0) goto 170
5768 ! check for too many overlaps with sphere of interest
5770 if (io .ge. maxarc) then
5772 20 format (/,' SURFATOM -- Increase the Value of MAXARC')
5776 ! get overlap between current sphere and sphere of interest
5785 gr(io) = (ccsq+rplus*rminus) / (2.0d0*rr*b1(io))
5791 ! case where no other spheres overlap the sphere of interest
5794 area = 4.0d0 * pi * rrsq
5798 ! case where only one sphere overlaps the sphere of interest
5801 area = pix2 * (1.0d0 + gr(1))
5802 area = mod(area,4.0d0*pi) * rrsq
5806 ! case where many spheres intersect the sphere of interest;
5807 ! sort the intersecting spheres by their degree of overlap
5809 call sort2 (io,gr,key)
5812 intag(i) = intag1(k)
5821 ! get radius of each overlap circle on surface of the sphere
5826 risq(i) = rrsq - gi*gi
5827 ri(i) = sqrt(risq(i))
5828 ther(i) = 0.5d0*pi - asin(min(1.0d0,max(-1.0d0,gr(i))))
5831 ! find boundary of inaccessible area on sphere of interest
5834 if (.not. omit(k)) then
5841 ! check to see if J circle is intersecting K circle;
5842 ! get distance between circle centers and sum of radii
5845 if (omit(j)) goto 60
5846 cc = (txk*xc(j)+tyk*yc(j)+tzk*zc(j))/(bk*b(j))
5847 cc = acos(min(1.0d0,max(-1.0d0,cc)))
5848 td = therk + ther(j)
5850 ! check to see if circles enclose separate regions
5852 if (cc .ge. td) goto 60
5854 ! check for circle J completely inside circle K
5856 if (cc+ther(j) .lt. therk) goto 40
5858 ! check for circles that are essentially parallel
5860 if (cc .gt. delta) goto 50
5865 ! check to see if sphere of interest is completely buried
5868 if (pix2-cc .le. td) goto 170
5874 ! find T value of circle intersections
5877 if (omit(k)) goto 110
5892 ! rotation matrix elements
5904 if (.not. omit(j)) then
5909 ! rotate spheres so K vector colinear with z-axis
5911 uxj = txj*axx + tyj*axy - tzj*axz
5912 uyj = tyj*ayy - txj*ayx
5913 uzj = txj*azx + tyj*azy + tzj*azz
5914 cosine = min(1.0d0,max(-1.0d0,uzj/b(j)))
5915 if (acos(cosine) .lt. therk+ther(j)) then
5916 dsqj = uxj*uxj + uyj*uyj
5921 tr2 = risqk*dsqj - tb*tb
5927 ! get T values of intersection for K circle
5930 tb = min(1.0d0,max(-1.0d0,tb))
5932 if (tyb-txr .lt. 0.0d0) tk1 = pix2 - tk1
5934 tb = min(1.0d0,max(-1.0d0,tb))
5936 if (tyb+txr .lt. 0.0d0) tk2 = pix2 - tk2
5937 thec = (rrsq*uzj-gk*bg(j)) / (rik*ri(j)*b(j))
5938 if (abs(thec) .lt. 1.0d0) then
5940 else if (thec .ge. 1.0d0) then
5942 else if (thec .le. -1.0d0) then
5946 ! see if "tk1" is entry or exit point; check t=0 point;
5947 ! "ti" is exit point, "tf" is entry point
5949 cosine = min(1.0d0,max(-1.0d0, &
5950 (uzj*gk-uxj*rik)/(b(j)*rr)))
5951 if ((acos(cosine)-ther(j))*(tk2-tk1) .le. 0.0d0) then
5959 if (narc .ge. maxarc) then
5961 70 format (/,' SURFATOM -- Increase the Value',&
5965 if (tf .le. ti) then
5986 ! special case; K circle without intersections
5988 if (narc .le. 0) goto 90
5990 ! general case; sum up arclength and set connectivity code
5992 call sort2 (narc,arci,key)
5997 if (narc .gt. 1) then
6000 if (t .lt. arci(j)) then
6001 arcsum = arcsum + arci(j) - t
6002 exang = exang + ex(ni)
6004 if (jb .ge. maxarc) then
6006 80 format (/,' SURFATOM -- Increase the Value',&
6011 kent(jb) = maxarc*i + k
6013 kout(jb) = maxarc*k + i
6022 arcsum = arcsum + pix2 - t
6024 exang = exang + ex(ni)
6027 kent(jb) = maxarc*i + k
6029 kout(jb) = maxarc*k + i
6036 arclen = arclen + gr(k)*arcsum
6039 if (arclen .eq. 0.0d0) goto 170
6040 if (jb .eq. 0) goto 150
6042 ! find number of independent boundaries and check connectivity
6046 if (kout(k) .ne. 0) then
6053 if (m .eq. kent(ii)) then
6056 if (j .eq. jb) goto 150
6068 ! attempt to fix connectivity error by moving atom slightly
6072 140 format (/,' SURFATOM -- Connectivity Error at Atom',i6)
6081 ! compute the exposed surface area for the sphere of interest
6084 area = ib*pix2 + exang + arclen
6085 area = mod(area,4.0d0*pi) * rrsq
6087 ! attempt to fix negative area by moving atom slightly
6089 if (area .lt. 0.0d0) then
6092 160 format (/,' SURFATOM -- Negative Area at Atom',i6)
6103 end subroutine surfatom
6104 !----------------------------------------------------------------
6105 !----------------------------------------------------------------
6106 subroutine alloc_MD_arrays
6107 !EL Allocation of arrays used by MD module
6109 integer :: nres2,nres6
6112 !----------------------
6116 allocate(friction(3,0:nres2),stochforc(3,0:nres2)) !(3,0:MAXRES2)
6117 allocate(fric_work(nres6),stoch_work(nres6),fricgam(nres6)) !(MAXRES6)
6118 if(.not.allocated(fricmat)) allocate(fricmat(nres2,nres2))
6119 allocate(fricvec(nres2,nres2))
6120 allocate(pfric_mat(nres2,nres2),vfric_mat(nres2,nres2))
6121 allocate(afric_mat(nres2,nres2),prand_mat(nres2,nres2))
6122 allocate(vrand_mat1(nres2,nres2),vrand_mat2(nres2,nres2)) !(MAXRES2,MAXRES2)
6123 allocate(pfric0_mat(nres2,nres2,0:maxflag_stoch))
6124 allocate(afric0_mat(nres2,nres2,0:maxflag_stoch))
6125 allocate(vfric0_mat(nres2,nres2,0:maxflag_stoch))
6126 allocate(prand0_mat(nres2,nres2,0:maxflag_stoch))
6127 allocate(vrand0_mat1(nres2,nres2,0:maxflag_stoch))
6128 allocate(vrand0_mat2(nres2,nres2,0:maxflag_stoch)) !(MAXRES2,MAXRES2,0:maxflag_stoch)
6129 allocate(flag_stoch(0:maxflag_stoch)) !(0:maxflag_stoch)
6131 allocate(mt1(nres2,nres2),mt2(nres2,nres2),mt3(nres2,nres2)) !(maxres2,maxres2)
6132 !----------------------
6134 ! commom.langevin.lang0
6136 allocate(friction(3,0:nres2),stochforc(3,0:nres2)) !(3,0:MAXRES2)
6137 if(.not.allocated(fricmat)) allocate(fricmat(nres2,nres2))
6138 allocate(fricvec(nres2,nres2)) !(MAXRES2,MAXRES2)
6139 allocate(fric_work(nres6),stoch_work(nres6),fricgam(nres6)) !(MAXRES6)
6140 allocate(flag_stoch(0:maxflag_stoch)) !(0:maxflag_stoch)
6143 if(.not.allocated(fcopy)) allocate(fcopy(nres2,nres2))
6144 !----------------------
6145 ! commom.hairpin in CSA module
6146 !----------------------
6147 ! common.mce in MCM_MD module
6148 !----------------------
6150 ! common /mdgrad/ in module.energy
6151 ! common /back_constr/ in module.energy
6152 ! common /qmeas/ in module.energy
6155 allocate(potEcomp(0:n_ene+4)) !(0:n_ene+4)
6157 allocate(d_t(3,0:nres2),d_a(3,0:nres2),d_t_old(3,0:nres2)) !(3,0:MAXRES2)
6158 allocate(d_a_work(nres6)) !(6*MAXRES)
6160 allocate(DM(nres2),DU1(nres2),DU2(nres2))
6161 allocate(DMorig(nres2),DU1orig(nres2),DU2orig(nres2))
6163 allocate(Gmat(nres2,nres2),A(nres2,nres2))
6164 if(.not.allocated(Ginv)) allocate(Ginv(nres2,nres2)) !in control: ergastulum
6165 allocate(Gsqrp(nres2,nres2),Gsqrm(nres2,nres2),Gvec(nres2,nres2)) !(maxres2,maxres2)
6167 allocate(Geigen(nres2)) !(maxres2)
6168 if(.not.allocated(vtot)) allocate(vtot(nres2)) !(maxres2)
6169 ! common /inertia/ in io_conf: parmread
6170 ! real(kind=8),dimension(:),allocatable :: ISC,msc !(ntyp+1)
6171 ! common /langevin/in io read_MDpar
6172 ! real(kind=8),dimension(:),allocatable :: gamsc !(ntyp1)
6173 ! real(kind=8),dimension(:),allocatable :: stdfsc !(ntyp)
6174 ! in io_conf: parmread
6175 ! real(kind=8),dimension(:),allocatable :: restok !(ntyp+1)
6176 ! common /mdpmpi/ in control: ergastulum
6177 if(.not.allocated(ng_start)) allocate(ng_start(0:nfgtasks-1))
6178 if(.not.allocated(ng_counts)) allocate(ng_counts(0:nfgtasks-1))
6179 if(.not.allocated(nginv_counts)) allocate(nginv_counts(0:nfgtasks-1)) !(0:MaxProcs-1)
6180 if(.not.allocated(nginv_start)) allocate(nginv_start(0:nfgtasks)) !(0:MaxProcs)
6181 !----------------------
6182 ! common.muca in read_muca
6183 ! common /double_muca/
6184 ! real(kind=8) :: elow,ehigh,factor,hbin,factor_min
6185 ! real(kind=8),dimension(:),allocatable :: emuca,nemuca,&
6186 ! nemuca2,hist !(4*maxres)
6187 ! common /integer_muca/
6188 ! integer :: nmuca,imtime,muca_smooth
6190 ! real(kind=8),dimension(:),allocatable :: elowi,ehighi !(maxprocs)
6191 !----------------------
6193 ! common /mdgrad/ in module.energy
6194 ! common /back_constr/ in module.energy
6195 ! common /qmeas/ in module.energy
6199 allocate(d_t_work(nres6),d_t_work_new(nres6),d_af_work(nres6))
6200 allocate(d_as_work(nres6),kinetic_force(nres6)) !(MAXRES6)
6201 allocate(d_t_new(3,0:nres2),d_a_old(3,0:nres2),d_a_short(3,0:nres2)) !,d_a !(3,0:MAXRES2)
6202 allocate(stdforcp(nres),stdforcsc(nres)) !(MAXRES)
6203 !----------------------
6205 allocate(D_ban(nres6)) !(MAXRES6) maxres6=6*maxres
6206 ! common /stochcalc/ stochforcvec
6207 allocate(stochforcvec(nres6)) !(MAXRES6) maxres6=6*maxres
6208 !----------------------
6210 end subroutine alloc_MD_arrays
6211 !-----------------------------------------------------------------------------
6212 !-----------------------------------------------------------------------------