From e12c8db731e266c6e38b2f5883f3ae7c15bbfb98 Mon Sep 17 00:00:00 2001 From: Adam Sieradzan Date: Mon, 8 May 2017 09:48:01 +0200 Subject: [PATCH] small changes --- ..._ext.1gab_3S_qclass5no310-shan2-sc-16-10-8k_lip | 2 +- PARAM/sc_GB_opt_ext_lip.7p_wham_last | 2 +- PARAM/sc_GB_opt_ext_lip.7p_wham_last_four | 2 +- PARAM/sc_GB_opt_iter0_7prot-eps_ext_lip.parm | 2 +- PARAM/scinter_GB_ext_lip.parm | 2 +- PARAM/tube.parm | 4 +++ source/cluster/wham/src-M/COMMON.SHIELD | 5 ++- source/cluster/wham/src-M/energy_p_new.F | 33 ++++++++++++++++++-- source/cluster/wham/src-M/readrtns.F | 5 +++ source/unres/src_MD-M/energy_p_new-sep_barrier.F | 2 +- source/unres/src_MD-M/energy_p_new_barrier.F | 21 ++++++++----- source/unres/src_MD-M/unres.F | 16 +++++----- 12 files changed, 70 insertions(+), 26 deletions(-) diff --git a/PARAM/sc_GB_opt_ext.1gab_3S_qclass5no310-shan2-sc-16-10-8k_lip b/PARAM/sc_GB_opt_ext.1gab_3S_qclass5no310-shan2-sc-16-10-8k_lip index 9708c27..2abb67a 100644 --- a/PARAM/sc_GB_opt_ext.1gab_3S_qclass5no310-shan2-sc-16-10-8k_lip +++ b/PARAM/sc_GB_opt_ext.1gab_3S_qclass5no310-shan2-sc-16-10-8k_lip @@ -228,7 +228,7 @@ -0.1779 −3.4493 3.360749 4.211903 5.240276 3.016734 3.016734 - -6.5557 2.905459 3.641304 4.530360 + -9.4378 2.905459 3.641304 4.530360 2.608049 2.608049 2.252800 2.823350 3.512697 2.022197 diff --git a/PARAM/sc_GB_opt_ext_lip.7p_wham_last b/PARAM/sc_GB_opt_ext_lip.7p_wham_last index f006f35..4f1f32f 100644 --- a/PARAM/sc_GB_opt_ext_lip.7p_wham_last +++ b/PARAM/sc_GB_opt_ext_lip.7p_wham_last @@ -229,7 +229,7 @@ -0.1779 -3.4493 3.360749 4.211903 5.240276 3.016734 3.016734 - -6.5557 2.905459 3.641304 4.530360 + -9.4378 2.905459 3.641304 4.530360 2.608049 2.608049 2.252800 2.823350 3.512697 2.022197 diff --git a/PARAM/sc_GB_opt_ext_lip.7p_wham_last_four b/PARAM/sc_GB_opt_ext_lip.7p_wham_last_four index f99e603..59180ac 100644 --- a/PARAM/sc_GB_opt_ext_lip.7p_wham_last_four +++ b/PARAM/sc_GB_opt_ext_lip.7p_wham_last_four @@ -229,7 +229,7 @@ -0.1779 -3.4493 3.360749 4.211903 5.240276 3.016734 3.016734 - -6.5557 2.905459 3.641304 4.530360 + -9.4378 2.905459 3.641304 4.530360 2.608049 2.608049 2.252800 2.823350 3.512697 2.022197 diff --git a/PARAM/sc_GB_opt_iter0_7prot-eps_ext_lip.parm b/PARAM/sc_GB_opt_iter0_7prot-eps_ext_lip.parm index a4e97f6..c97df64 100644 --- a/PARAM/sc_GB_opt_iter0_7prot-eps_ext_lip.parm +++ b/PARAM/sc_GB_opt_iter0_7prot-eps_ext_lip.parm @@ -232,7 +232,7 @@ -0.1779 -3.4493 3.360749 4.211903 5.240276 3.016734 3.016734 - -6.5557 2.905459 3.641304 4.530360 + -9.4379 2.905459 3.641304 4.530360 2.608049 2.608049 2.252800 2.823350 3.512697 2.022197 diff --git a/PARAM/scinter_GB_ext_lip.parm b/PARAM/scinter_GB_ext_lip.parm index e600c30..6b31b91 100644 --- a/PARAM/scinter_GB_ext_lip.parm +++ b/PARAM/scinter_GB_ext_lip.parm @@ -229,7 +229,7 @@ -0.1779 -3.4493 3.360749 4.211903 5.240276 3.016734 3.016734 - -6.5557 2.905459 3.641304 4.530360 + -9.4378 2.905459 3.641304 4.530360 2.608049 2.608049 2.252800 2.823350 3.512697 2.022197 diff --git a/PARAM/tube.parm b/PARAM/tube.parm index d3f9616..efae7fd 100644 --- a/PARAM/tube.parm +++ b/PARAM/tube.parm @@ -22,3 +22,7 @@ 6.6424306340 5.2914044780 5.2914044780 + 0.0 + 0.0 + 0.0 + 0.0 diff --git a/source/cluster/wham/src-M/COMMON.SHIELD b/source/cluster/wham/src-M/COMMON.SHIELD index 1f96c94..0fb02ed 100644 --- a/source/cluster/wham/src-M/COMMON.SHIELD +++ b/source/cluster/wham/src-M/COMMON.SHIELD @@ -1,10 +1,13 @@ double precision VSolvSphere,VSolvSphere_div,long_r_sidechain, & short_r_sidechain,fac_shield,grad_shield_side,grad_shield, - & buff_shield,wshield,grad_shield_loc + & buff_shield,wshield,grad_shield_loc,lipscale,sslipi,sslipj, + & ssgradlipi,ssgradlipj integer ishield_list,shield_list,ees0plist common /shield/ VSolvSphere,VSolvSphere_div,buff_shield, & long_r_sidechain(ntyp), & short_r_sidechain(ntyp),fac_shield(maxres),wshield, + & sslipi,sslipj,lipscale, + & ssgradlipi,ssgradlipj, & grad_shield_side(3,maxcont,-1:maxres),grad_shield(3,-1:maxres), & grad_shield_loc(3,maxcont,-1:maxres), & ishield_list(maxres),shield_list(maxcont,maxres), diff --git a/source/cluster/wham/src-M/energy_p_new.F b/source/cluster/wham/src-M/energy_p_new.F index dfdaba6..e7759b2 100644 --- a/source/cluster/wham/src-M/energy_p_new.F +++ b/source/cluster/wham/src-M/energy_p_new.F @@ -2349,6 +2349,7 @@ C#undef DEBUG el1=el1*fac_shield(i)**2*fac_shield(j)**2 el2=el2*fac_shield(i)**2*fac_shield(j)**2 eesij=(el1+el2) + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) ees=ees+eesij else fac_shield(i)=1.0 @@ -2358,6 +2359,7 @@ C#undef DEBUG endif C ees=ees+eesij evdw1=evdw1+evdwij*sss + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) cd write(iout,'(2(2i3,2x),7(1pd12.4)/2(3(1pd12.4),5x)/)') cd & iteli,i,itelj,j,aaa,bbb,ael6i,ael3i, cd & 1.0D0/dsqrt(rrmij),evdwij,eesij, @@ -2788,6 +2790,8 @@ C fac_shield(j)=0.6 endif eel_loc_ij=eel_loc_ij & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + eel_loc=eel_loc+eel_loc_ij C Partial derivatives in virtual-bond dihedral angles gamma if (calc_grad) then @@ -2852,9 +2856,10 @@ cd write(iout,*) 'aggj1',aggj1 C Derivatives of eello in DC(i+1) thru DC(j-1) or DC(nres-2) do l=1,3 - ggg(l)=agg(l,1)*muij(1)+ - & agg(l,2)*muij(2)+agg(l,3)*muij(3)+agg(l,4)*muij(4) + ggg(l)=(agg(l,1)*muij(1)+ + & agg(l,2)*muij(2)+agg(l,3)*muij(3)+agg(l,4)*muij(4)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) enddo do k=i+2,j2 @@ -2867,18 +2872,22 @@ C Remaining derivatives of eello gel_loc(l,i)=gel_loc(l,i)+aggi(l,1)*muij(1)+ & aggi(l,2)*muij(2)+aggi(l,3)*muij(3)+aggi(l,4)*muij(4) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) gel_loc(l,i+1)=gel_loc(l,i+1)+aggi1(l,1)*muij(1)+ & aggi1(l,2)*muij(2)+aggi1(l,3)*muij(3)+aggi1(l,4)*muij(4) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) gel_loc(l,j)=gel_loc(l,j)+aggj(l,1)*muij(1)+ & aggj(l,2)*muij(2)+aggj(l,3)*muij(3)+aggj(l,4)*muij(4) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) gel_loc(l,j1)=gel_loc(l,j1)+aggj1(l,1)*muij(1)+ & aggj1(l,2)*muij(2)+aggj1(l,3)*muij(3)+aggj1(l,4)*muij(4) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) enddo endif @@ -3178,8 +3187,11 @@ C fac_shield(j)=0.6 endif eello_turn3=eello_turn3+0.5d0*(pizda(1,1)+pizda(2,2)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) + eello_t3=0.5d0*(pizda(1,1)+pizda(2,2)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) cd write (2,*) 'i,',i,' j',j,'eello_turn3', cd & 0.5d0*(pizda(1,1)+pizda(2,2)), @@ -3253,6 +3265,7 @@ C Cartesian derivatives gcorr3_turn(l,i)=gcorr3_turn(l,i) & +0.5d0*(pizda(1,1)+pizda(2,2)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) a_temp(1,1)=aggi1(l,1) a_temp(1,2)=aggi1(l,2) @@ -3262,6 +3275,7 @@ C Cartesian derivatives gcorr3_turn(l,i+1)=gcorr3_turn(l,i+1) & +0.5d0*(pizda(1,1)+pizda(2,2)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) a_temp(1,1)=aggj(l,1) a_temp(1,2)=aggj(l,2) @@ -3271,6 +3285,7 @@ C Cartesian derivatives gcorr3_turn(l,j)=gcorr3_turn(l,j) & +0.5d0*(pizda(1,1)+pizda(2,2)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) a_temp(1,1)=aggj1(l,1) a_temp(1,2)=aggj1(l,2) @@ -3280,6 +3295,7 @@ C Cartesian derivatives gcorr3_turn(l,j1)=gcorr3_turn(l,j1) & +0.5d0*(pizda(1,1)+pizda(2,2)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) enddo endif @@ -3333,8 +3349,11 @@ C fac_shield(j)=0.6 endif eello_turn4=eello_turn4-(s1+s2+s3) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) + eello_t4=-(s1+s2+s3) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) cd write (2,*) 'i,',i,' j',j,'eello_turn4',-(s1+s2+s3), cd & ' eello_turn4_num',8*eello_turn4_num @@ -3390,6 +3409,7 @@ C & *2.0 s3=0.5d0*(pizda(1,1)+pizda(2,2)) gel_loc_turn4(i)=gel_loc_turn4(i)-(s1+s3) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) C Derivatives in gamma(i+1) call transpose2(EUgder(1,1,i+2),e2tder(1,1)) @@ -3400,6 +3420,7 @@ C Derivatives in gamma(i+1) s3=0.5d0*(pizda(1,1)+pizda(2,2)) gel_loc_turn4(i+1)=gel_loc_turn4(i+1)-(s2+s3) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) C Derivatives in gamma(i+2) call transpose2(EUgder(1,1,i+3),e3tder(1,1)) @@ -3413,7 +3434,8 @@ C Derivatives in gamma(i+2) s3=0.5d0*(pizda(1,1)+pizda(2,2)) gel_loc_turn4(i+2)=gel_loc_turn4(i+2)-(s1+s2+s3) & *fac_shield(i)*fac_shield(j) - + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) + C Cartesian derivatives C Derivatives of this turn contributions in DC(i+2) if (j.lt.nres-1) then @@ -3434,6 +3456,7 @@ C Derivatives of this turn contributions in DC(i+2) ggg(l)=-(s1+s2+s3) gcorr4_turn(l,i+2)=gcorr4_turn(l,i+2)-(s1+s2+s3) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) enddo endif @@ -3454,6 +3477,7 @@ C Remaining derivatives of this turn contribution s3=0.5d0*(pizda(1,1)+pizda(2,2)) gcorr4_turn(l,i)=gcorr4_turn(l,i)-(s1+s2+s3) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) a_temp(1,1)=aggi1(l,1) a_temp(1,2)=aggi1(l,2) @@ -3470,6 +3494,7 @@ C Remaining derivatives of this turn contribution s3=0.5d0*(pizda(1,1)+pizda(2,2)) gcorr4_turn(l,i+1)=gcorr4_turn(l,i+1)-(s1+s2+s3) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) a_temp(1,1)=aggj(l,1) a_temp(1,2)=aggj(l,2) @@ -3486,6 +3511,7 @@ C Remaining derivatives of this turn contribution s3=0.5d0*(pizda(1,1)+pizda(2,2)) gcorr4_turn(l,j)=gcorr4_turn(l,j)-(s1+s2+s3) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) a_temp(1,1)=aggj1(l,1) a_temp(1,2)=aggj1(l,2) @@ -3502,6 +3528,7 @@ C Remaining derivatives of this turn contribution s3=0.5d0*(pizda(1,1)+pizda(2,2)) gcorr4_turn(l,j1)=gcorr4_turn(l,j1)-(s1+s2+s3) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0) enddo endif diff --git a/source/cluster/wham/src-M/readrtns.F b/source/cluster/wham/src-M/readrtns.F index 63e0206..21a2b76 100644 --- a/source/cluster/wham/src-M/readrtns.F +++ b/source/cluster/wham/src-M/readrtns.F @@ -208,6 +208,7 @@ C call reada(weightcard,'WSC',wsc,1.0d0) write(iout,*) 'WSHIELD',wshield call reada(weightcard,'WTUBE',wtube,0.0d0) write(iout,*) 'WTUBE',wtube + call reada(weightcard,"LIPSCALE",lipscale,1.3D0) call reada(weightcard,'WLT',wliptran,0.0D0) call reada(weightcard,"ATRISS",atriss,0.301D0) call reada(weightcard,"BTRISS",btriss,0.021D0) @@ -217,6 +218,10 @@ C call reada(weightcard,'WSC',wsc,1.0d0) write (iout,*) "BTRISS=", btriss write (iout,*) "CTRISS=", ctriss write (iout,*) "DTRISS=", dtriss + if (shield_mode.gt.0) then + lipscale=0.0d0 + write (iout,*) "WARNING:liscale not used in shield mode" + endif dyn_ss=(index(weightcard,'DYN_SS').gt.0) do i=1,maxres dyn_ss_mask(i)=.false. diff --git a/source/unres/src_MD-M/energy_p_new-sep_barrier.F b/source/unres/src_MD-M/energy_p_new-sep_barrier.F index 44384a6..99b0bc2 100644 --- a/source/unres/src_MD-M/energy_p_new-sep_barrier.F +++ b/source/unres/src_MD-M/energy_p_new-sep_barrier.F @@ -841,7 +841,7 @@ C Calculate gradient components. fac=-expon*(e1+evdwij)*rij_shift sigder=fac*sigder fac=rij*fac - fac=fac+evdwij/(1.0-sss)*(-sssgrad)/sigmaii(itypi,itypj)*rij + fac=fac+evdwij/sss*(-sssgrad)/sigmaii(itypi,itypj)*rij c fac=0.0d0 C Calculate the radial part of the gradient gg(1)=xj*fac diff --git a/source/unres/src_MD-M/energy_p_new_barrier.F b/source/unres/src_MD-M/energy_p_new_barrier.F index e3a17dd..3703b07 100644 --- a/source/unres/src_MD-M/energy_p_new_barrier.F +++ b/source/unres/src_MD-M/energy_p_new_barrier.F @@ -3692,13 +3692,13 @@ c if ((zmedi.gt.((0.5d0)*boxzsize)).or. c & (zmedi.lt.((-0.5d0)*boxzsize))) then c go to 196 c endif - xmedi=mod(xmedi,boxxsize) + xmedi=dmod(xmedi,boxxsize) if (xmedi.lt.0) xmedi=xmedi+boxxsize - ymedi=mod(ymedi,boxysize) + ymedi=dmod(ymedi,boxysize) if (ymedi.lt.0) ymedi=ymedi+boxysize - zmedi=mod(zmedi,boxzsize) + zmedi=dmod(zmedi,boxzsize) if (zmedi.lt.0) zmedi=zmedi+boxzsize - zmedi2=mod(zmedi,boxzsize) + zmedi2=dmod(zmedi,boxzsize) if (zmedi2.lt.0) zmedi2=zmedi2+boxzsize if ((zmedi2.gt.bordlipbot) &.and.(zmedi2.lt.bordliptop)) then @@ -3757,11 +3757,11 @@ c & .or. itype(i-1).eq.ntyp1 xmedi=c(1,i)+0.5d0*dxi ymedi=c(2,i)+0.5d0*dyi zmedi=c(3,i)+0.5d0*dzi - xmedi=mod(xmedi,boxxsize) + xmedi=dmod(xmedi,boxxsize) if (xmedi.lt.0) xmedi=xmedi+boxxsize - ymedi=mod(ymedi,boxysize) + ymedi=dmod(ymedi,boxysize) if (ymedi.lt.0) ymedi=ymedi+boxysize - zmedi=mod(zmedi,boxzsize) + zmedi=dmod(zmedi,boxzsize) if (zmedi.lt.0) zmedi=zmedi+boxzsize if ((zmedi.gt.bordlipbot) &.and.(zmedi.lt.bordliptop)) then @@ -3965,6 +3965,7 @@ C lipbufthick is thickenes of lipid buffore enddo enddo if (isubchap.eq.1) then +C print *,i,j xj=xj_temp-xmedi yj=yj_temp-ymedi zj=zj_temp-zmedi @@ -4173,10 +4174,14 @@ C print *,"bafter", gelc_long(1,i), gelc_long(1,j) C Lipidic part for lipscale gelc_long(3,j)=gelc_long(3,j)+ & ssgradlipj*eesij/2.0d0*lipscale**2 - +C if ((ssgradlipj*eesij/2.0d0*lipscale**2).ne.0.0 ) +C & write(iout,*) "WTF",j gelc_long(3,i)=gelc_long(3,i)+ & ssgradlipi*eesij/2.0d0*lipscale**2 +C if ((ssgradlipi*eesij/2.0d0*lipscale**2).ne.0.0 ) +C & write(iout,*) "WTF",i + * * Loop over residues i+1 thru j-1. * diff --git a/source/unres/src_MD-M/unres.F b/source/unres/src_MD-M/unres.F index f51b2d7..59c6b64 100644 --- a/source/unres/src_MD-M/unres.F +++ b/source/unres/src_MD-M/unres.F @@ -140,11 +140,11 @@ c if (me.eq.king .or. .not. out1file) then c write (iout,*) "Calling chainbuild" c call flush(iout) c endif - call chainbuild -c if (me.eq.king .or. .not. out1file) then -c write (iout,*) "Calling MD" -c call flush(iout) -c endif +! call chainbuild + if (me.eq.king .or. .not. out1file) then + write (iout,*) "Calling MD" + call flush(iout) + endif call MD return end @@ -159,9 +159,9 @@ c--------------------------------------------------------------------------- include 'COMMON.CONTROL' include 'COMMON.IOUNITS' include 'COMMON.REMD' - if (me.eq.king .or. .not. out1file) - & write (iout,*) "Calling chainbuild" - call chainbuild +! if (me.eq.king .or. .not. out1file) +! & write (iout,*) "Calling chainbuild" +! call chainbuild if (me.eq.king .or. .not. out1file) & write (iout,*) "Calling REMD" if (remd_mlist) then -- 1.7.9.5