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author
Adam Sieradzan
<adasko@piasek4.chem.univ.gda.pl>
Mon, 8 May 2017 07:48:01 +0000
(09:48 +0200)
committer
Adam Sieradzan
<adasko@piasek4.chem.univ.gda.pl>
Mon, 8 May 2017 07:48:01 +0000
(09:48 +0200)
12 files changed:
PARAM/sc_GB_opt_ext.1gab_3S_qclass5no310-shan2-sc-16-10-8k_lip
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PARAM/sc_GB_opt_ext_lip.7p_wham_last
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PARAM/sc_GB_opt_ext_lip.7p_wham_last_four
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PARAM/sc_GB_opt_iter0_7prot-eps_ext_lip.parm
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PARAM/scinter_GB_ext_lip.parm
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PARAM/tube.parm
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source/cluster/wham/src-M/COMMON.SHIELD
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source/cluster/wham/src-M/energy_p_new.F
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source/cluster/wham/src-M/readrtns.F
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source/unres/src_MD-M/energy_p_new-sep_barrier.F
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source/unres/src_MD-M/energy_p_new_barrier.F
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source/unres/src_MD-M/unres.F
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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
(file)
--- 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
-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
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
(file)
--- 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
-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
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
(file)
--- 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
-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
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
(file)
--- 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
-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
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
(file)
--- 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
-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
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
(file)
--- a/
PARAM/tube.parm
+++ b/
PARAM/tube.parm
@@
-22,3
+22,7
@@
6.6424306340
5.2914044780
5.2914044780
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
(file)
--- 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,
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,
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),
& 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
(file)
--- 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)
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
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
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,
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)
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
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
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)
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
enddo
do k=i+2,j2
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)
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)
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)
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)
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
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)
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)
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)),
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)
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)
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)
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)
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)
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)
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)
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
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)
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)
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
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)
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))
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)
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))
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)
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
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)
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
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)
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)
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)
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)
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)
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)
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)
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
enddo
endif
diff --git
a/source/cluster/wham/src-M/readrtns.F
b/source/cluster/wham/src-M/readrtns.F
index
63e0206
..
21a2b76
100644
(file)
--- 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
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)
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
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.
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
(file)
--- 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=-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
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
(file)
--- 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
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
if (xmedi.lt.0) xmedi=xmedi+boxxsize
- ymedi=mod(ymedi,boxysize)
+ ymedi=dmod(ymedi,boxysize)
if (ymedi.lt.0) ymedi=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.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
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=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
if (xmedi.lt.0) xmedi=xmedi+boxxsize
- ymedi=mod(ymedi,boxysize)
+ ymedi=dmod(ymedi,boxysize)
if (ymedi.lt.0) ymedi=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
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
enddo
enddo
if (isubchap.eq.1) then
+C print *,i,j
xj=xj_temp-xmedi
yj=yj_temp-ymedi
zj=zj_temp-zmedi
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 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
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.
*
*
* 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
(file)
--- 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
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
call MD
return
end
@@
-159,9
+159,9
@@
c---------------------------------------------------------------------------
include 'COMMON.CONTROL'
include 'COMMON.IOUNITS'
include 'COMMON.REMD'
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
if (me.eq.king .or. .not. out1file)
& write (iout,*) "Calling REMD"
if (remd_mlist) then