add_subdirectory(source/cluster/unres/src)
add_subdirectory(source/xdrfpdb/src)
add_subdirectory(source/xdrfpdb/src-M)
- add_subdirectory(source/maxlik/src_CSA)
+# add_subdirectory(source/maxlik/src_CSA)
else()
add_subdirectory(source/unres/src_MD)
--- /dev/null
+ 0.02
+ -2.09251
+ -1.67129
+ -2.43220
+ -2.44579
+ -2.30991
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+ 0.00000
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+ 0.05435
+ 0.29893
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+ 1.34518
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+ -1.67129
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+ -0.35328
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.0278930397 .0076922911 .1033536738 -.0098256036
.0611385674 .0448303346 .0861379100 .0861379100
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+
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+ 5.8845382769
+
+ 7.0106342493 6.8341607204 6.2047876082 5.5802122247
+ 5.6716968726 5.2011344932 4.1966522349 4.2383931955
+ 3.8954073453 3.5679086118 3.1136348127 2.7622561241
+ 4.5092053374 4.0238412606 3.9799853578 4.8087180377
+ 6.8378960152 6.9241225787 5.6716968726 5.6716968726
+
+ 6.5353606708 5.8844482033 5.1100976261 5.5515360893
+ 4.9587559238 4.2030790774 4.0351600709 3.6506289806
+ 3.4640416936 3.1611022087 2.7976192835 4.0422832763
+ 3.4415952740 3.8620694983 4.5934246009 6.3512039986
+ 6.5291325353 5.5515360893 5.5515360893
+
+ 5.2828811325 4.8298466315 4.7575327777 4.7249779042
+ 3.5656384285 3.5613366567 3.9273045564 3.7664779118
+ 3.5861699761 3.5523191627 4.6508672463 4.2424308260
+ 4.0987727783 4.5079669929 6.1425192423 6.1394821460
+ 4.7575327777 4.7575327777
+
+ 4.2222645754 4.1627149417 3.9786372270 3.1623319201
+ 2.9379696734 3.1365985188 2.8025851476 2.6576343487
+ 2.8733395837 3.8785891655 3.4443068252 3.4405132673
+ 4.0915305763 5.5200206406 5.4415971840 4.1627149417
+ 4.1627149417
+
+ 4.3860654351 3.6520014167 3.0264937881 2.5680579493
+ 2.5001857370 2.1393094782 1.4707077389 1.7373181916
+ 3.1045342752 2.0152329038 1.8196209136 3.6395852546
+ 5.4858936024 5.2914044780 4.3860654351 4.3860654351
+
+ 2.5016557935 2.7879606493 2.1424756816 1.0741544747
+ 1.3236438850 -.2712356678 .7613312181 2.8627348285
+ 1.5002127649 -.2392577636 3.5381128985 4.9382573262
+ 4.7881880526 3.6520014167 3.6520014167
+
+ 2.2903847447 2.2466771550 1.5053607856 1.4031797188
+ .9676209687 1.3075541842 2.8595118604 1.9833053538
+ -.0085773647 2.9557553666 4.2795129166 4.1302408718
+ 3.0264937881 3.0264937881
+
+ 1.2800038243 .7689806100 .9119606366 -.0744371793
+ .3669965427 2.4288563200 1.4975482174 -.2134101897
+ 2.9415021479 4.0534857018 3.9405275117 2.5680579493
+ 2.5680579493
+
+ -.6792428859 .4532383239 -.7590387660 -.3617034846
+ 1.6803275058 .6775209988 -.5354837468 2.6208591363
+ 4.2086428525 3.9022731880 2.5001857370 2.5001857370
+
+ .4136122500 -.1637152873 .2212564728 2.1287126020
+ .3896388275 -.2354089650 2.3255326077 3.5388086279
+ 3.6078928145 2.1393094782 2.1393094782
+
+ -3.5193531074 -2.0157307929 1.8355926160 2.7489174124
+ 2.0098391558 1.7975718667 3.4209730327 3.0809713206
+ 1.4707077389 1.4707077389
+
+ -1.3532688232 2.5504275249 2.8202873790 1.6253609671
+ 1.8625091247 2.7995744193 3.0182595342 1.7373181916
+ 1.7373181916
+
+ 3.7292778697 2.2944436481 -.0303565255 3.1115776177
+ 4.8164268553 4.7935507272 3.1045342752 3.1045342752
+
+ -.0827362961 -1.6043113182 2.4439837435 3.8790755071
+ 3.8711928134 2.0152329038 2.0152329038
+
+ -4.3897783280 2.3664634533 3.5878262177 3.6826168780
+ 1.8196209136 1.8196209136
+
+ 4.1927969260 4.6457432555 4.4872661030 3.6395852546
+ 3.6395852546
+
+ 6.6296746680 6.6717260508 5.4858936024 5.4858936024
+
+ 6.6424306340 5.2914044780 5.2914044780
+
+ 4.3860654351 4.3860654351
+
+ 4.3860654351
+
--- /dev/null
+4 6
+ 5.6053537261 6.2200032154 6.2159898496 6.4386968963
+ 6.2098101231 5.9596374798 5.4310222662 4.8790085257
+ 5.2638423822 5.4961954124 4.2928124162 4.3582250540
+ 4.2667755921 3.6813845958 3.5405429647 3.7026985912
+ 4.7177596156 3.3811992227 3.7936085458 4.5157490585
+ 6.2200032154 6.2159898496 5.2638423822 5.2638423822
+
+ 6.6296746680 6.6717260508 6.8168876945 6.8378960152
+ 6.3512039986 6.1425192423 5.5200206406 5.4858936024
+ 4.9382573262 4.2795129166 4.0534857018 4.2086428525
+ 3.5388086279 3.4209730327 2.7995744193 4.8164268553
+ 3.8790755071 3.5878262177 4.6457432555 6.6296746680
+ 6.6717260508 5.4858936024 5.4858936024
+
+ 6.6424306340 6.9715947250 6.9241225787 6.5291325353
+ 6.1394821460 5.4415971840 5.2914044780 4.7881880526
+ 4.1302408718 3.9405275117 3.9022731880 3.6078928145
+ 3.0809713206 3.0182595342 4.7935507272 3.8711928134
+ 3.6826168780 4.4872661030 6.6717260508 6.6424306340
+ 5.2914044780 5.2914044780
+
+ 7.3271707934 7.2970176793 7.0494948235 6.2565687662
+ 5.8133715113 5.8845382769 5.3463553241 4.7146928716
+ 4.4864793359 4.3092352779 3.6928361281 4.0100566871
+ 3.6584608489 4.5901676001 4.4681844010 4.6334334282
+ 4.9023945082 6.8168876945 6.9715947250 5.8845382769
+ 5.8845382769
+
+ 7.0106342493 6.8341607204 6.2047876082 5.5802122247
+ 5.6716968726 5.2011344932 4.1966522349 4.2383931955
+ 3.8954073453 3.5679086118 3.1136348127 2.7622561241
+ 4.5092053374 4.0238412606 3.9799853578 4.8087180377
+ 6.8378960152 6.9241225787 5.6716968726 5.6716968726
+
+ 6.5353606708 5.8844482033 5.1100976261 5.5515360893
+ 4.9587559238 4.2030790774 4.0351600709 3.6506289806
+ 3.4640416936 3.1611022087 2.7976192835 4.0422832763
+ 3.4415952740 3.8620694983 4.5934246009 6.3512039986
+ 6.5291325353 5.5515360893 5.5515360893
+
+ 5.2828811325 4.8298466315 4.7575327777 4.7249779042
+ 3.5656384285 3.5613366567 3.9273045564 3.7664779118
+ 3.5861699761 3.5523191627 4.6508672463 4.2424308260
+ 4.0987727783 4.5079669929 6.1425192423 6.1394821460
+ 4.7575327777 4.7575327777
+
+ 4.2222645754 4.1627149417 3.9786372270 3.1623319201
+ 2.9379696734 3.1365985188 2.8025851476 2.6576343487
+ 2.8733395837 3.8785891655 3.4443068252 3.4405132673
+ 4.0915305763 5.5200206406 5.4415971840 4.1627149417
+ 4.1627149417
+
+ 4.3860654351 3.6520014167 3.0264937881 2.5680579493
+ 2.5001857370 2.1393094782 1.4707077389 1.7373181916
+ 3.1045342752 2.0152329038 1.8196209136 3.6395852546
+ 5.4858936024 5.2914044780 4.3860654351 4.3860654351
+
+ 2.5016557935 2.7879606493 2.1424756816 1.0741544747
+ 1.3236438850 -.2712356678 .7613312181 2.8627348285
+ 1.5002127649 -.2392577636 3.5381128985 4.9382573262
+ 4.7881880526 3.6520014167 3.6520014167
+
+ 2.2903847447 2.2466771550 1.5053607856 1.4031797188
+ .9676209687 1.3075541842 2.8595118604 1.9833053538
+ -.0085773647 2.9557553666 4.2795129166 4.1302408718
+ 3.0264937881 3.0264937881
+
+ 1.2800038243 .7689806100 .9119606366 -.0744371793
+ .3669965427 2.4288563200 1.4975482174 -.2134101897
+ 2.9415021479 4.0534857018 3.9405275117 2.5680579493
+ 2.5680579493
+
+ -.6792428859 .4532383239 -.7590387660 -.3617034846
+ 1.6803275058 .6775209988 -.5354837468 2.6208591363
+ 4.2086428525 3.9022731880 2.5001857370 2.5001857370
+
+ .4136122500 -.1637152873 .2212564728 2.1287126020
+ .3896388275 -.2354089650 2.3255326077 3.5388086279
+ 3.6078928145 2.1393094782 2.1393094782
+
+ -3.5193531074 -2.0157307929 1.8355926160 2.7489174124
+ 2.0098391558 1.7975718667 3.4209730327 3.0809713206
+ 1.4707077389 1.4707077389
+
+ -1.3532688232 2.5504275249 2.8202873790 1.6253609671
+ 1.8625091247 2.7995744193 3.0182595342 1.7373181916
+ 1.7373181916
+
+ 3.7292778697 2.2944436481 -.0303565255 3.1115776177
+ 4.8164268553 4.7935507272 3.1045342752 3.1045342752
+
+ -.0827362961 -1.6043113182 2.4439837435 3.8790755071
+ 3.8711928134 2.0152329038 2.0152329038
+
+ -4.3897783280 2.3664634533 3.5878262177 3.6826168780
+ 1.8196209136 1.8196209136
+
+ 4.1927969260 4.6457432555 4.4872661030 3.6395852546
+ 3.6395852546
+
+ 6.6296746680 6.6717260508 5.4858936024 5.4858936024
+
+ 6.6424306340 5.2914044780 5.2914044780
+
+ 4.3860654351 4.3860654351
+
+ 4.3860654351
+
+ 2.6748060017 2.7338810145 2.9664647229 2.8819636737
+ 3.0210738150 2.8414286152 2.4773438660 2.4611943788
+ 2.4653201213 2.4925087371 2.5734767751 2.4564026744
+ 2.4847825281 2.4889289233 2.5089517645 2.5083338383
+ 2.4220622723 2.2714609770 2.4520703089 2.7026129788
+ 2.7338810145 2.9664647229 2.4653201213 2.4653201213
+
+ 4.9272154761 5.1054284230 4.2073516165 4.8513972837
+ 2.7848875293 3.5829861634 7.8660217576 7.4299209847
+ 1.9625939832 .7987769569 4.0580899681 1.8889021032
+ 3.1987197026 3.2673274538 2.6848131904 2.0043027404
+ 6.2446341910 8.1959452095 13.4748295858 2.6632376837
+ 5.1054284230 4.2073516165 1.9625939832 1.9625939832
+
+ .8699023011 1.0540660014 .9385909298 1.0263274101
+ 1.0835277045 1.0543183886 .7888686996 .8989305833
+ 1.0039962875 1.2427518128 .8932801724 .9173928990
+ 1.6157695657 1.4315860373 2.0498317879 1.4199615546
+ .9933677971 1.4319625600 27.4951763288 .7788025286
+ 1.0540660014 .9385909298 1.0039962875 1.0039962875
+
+ .0103697556 .0611385674 .0448303346 .0392831782
+ .0854166338 .0398896619 .0249496569 .0232410908
+ .0861379100 -.0754794185 -.0266146021 -.0163429099
+ .0572167103 -.0468608825 .0151048455 .0084963678
+ .0278930397 .0076922911 .1033536738 -.0098256036
+ .0611385674 .0448303346 .0861379100 .0861379100
+C From here are lipid
+ 5.6053537261 6.2200032154 6.2159898496 6.4386968963
+ 6.2098101231 5.9596374798 5.4310222662 4.8790085257
+ 5.2638423822 5.4961954124 4.2928124162 4.3582250540
+ 4.2667755921 3.6813845958 3.5405429647 3.7026985912
+ 4.7177596156 3.3811992227 3.7936085458 4.5157490585
+ 6.2200032154 6.2159898496 5.2638423822 5.2638423822
+
+ 6.6296746680 6.6717260508 6.8168876945 6.8378960152
+ 6.3512039986 6.1425192423 5.5200206406 5.4858936024
+ 4.9382573262 4.2795129166 4.0534857018 4.2086428525
+ 3.5388086279 3.4209730327 2.7995744193 4.8164268553
+ 3.8790755071 3.5878262177 4.6457432555 6.6296746680
+ 6.6717260508 5.4858936024 5.4858936024
+
+ 6.6424306340 6.9715947250 6.9241225787 6.5291325353
+ 6.1394821460 5.4415971840 5.2914044780 4.7881880526
+ 4.1302408718 3.9405275117 3.9022731880 3.6078928145
+ 3.0809713206 3.0182595342 4.7935507272 3.8711928134
+ 3.6826168780 4.4872661030 6.6717260508 6.6424306340
+ 5.2914044780 5.2914044780
+
+ 7.3271707934 7.2970176793 7.0494948235 6.2565687662
+ 5.8133715113 5.8845382769 5.3463553241 4.7146928716
+ 4.4864793359 4.3092352779 3.6928361281 4.0100566871
+ 3.6584608489 4.5901676001 4.4681844010 4.6334334282
+ 4.9023945082 6.8168876945 6.9715947250 5.8845382769
+ 5.8845382769
+
+ 7.0106342493 6.8341607204 6.2047876082 5.5802122247
+ 5.6716968726 5.2011344932 4.1966522349 4.2383931955
+ 3.8954073453 3.5679086118 3.1136348127 2.7622561241
+ 4.5092053374 4.0238412606 3.9799853578 4.8087180377
+ 6.8378960152 6.9241225787 5.6716968726 5.6716968726
+
+ 6.5353606708 5.8844482033 5.1100976261 5.5515360893
+ 4.9587559238 4.2030790774 4.0351600709 3.6506289806
+ 3.4640416936 3.1611022087 2.7976192835 4.0422832763
+ 3.4415952740 3.8620694983 4.5934246009 6.3512039986
+ 6.5291325353 5.5515360893 5.5515360893
+
+ 5.2828811325 4.8298466315 4.7575327777 4.7249779042
+ 3.5656384285 3.5613366567 3.9273045564 3.7664779118
+ 3.5861699761 3.5523191627 4.6508672463 4.2424308260
+ 4.0987727783 4.5079669929 6.1425192423 6.1394821460
+ 4.7575327777 4.7575327777
+
+ 4.2222645754 4.1627149417 3.9786372270 3.1623319201
+ 2.9379696734 3.1365985188 2.8025851476 2.6576343487
+ 2.8733395837 3.8785891655 3.4443068252 3.4405132673
+ 4.0915305763 5.5200206406 5.4415971840 4.1627149417
+ 4.1627149417
+
+ 4.3860654351 3.6520014167 3.0264937881 2.5680579493
+ 2.5001857370 2.1393094782 1.4707077389 1.7373181916
+ 3.1045342752 2.0152329038 1.8196209136 3.6395852546
+ 5.4858936024 5.2914044780 4.3860654351 4.3860654351
+
+ 2.5016557935 2.7879606493 2.1424756816 1.0741544747
+ 1.3236438850 -.2712356678 .7613312181 2.8627348285
+ 1.5002127649 -.2392577636 3.5381128985 4.9382573262
+ 4.7881880526 3.6520014167 3.6520014167
+
+ 2.2903847447 2.2466771550 1.5053607856 1.4031797188
+ .9676209687 1.3075541842 2.8595118604 1.9833053538
+ -.0085773647 2.9557553666 4.2795129166 4.1302408718
+ 3.0264937881 3.0264937881
+
+ 1.2800038243 .7689806100 .9119606366 -.0744371793
+ .3669965427 2.4288563200 1.4975482174 -.2134101897
+ 2.9415021479 4.0534857018 3.9405275117 2.5680579493
+ 2.5680579493
+
+ -.6792428859 .4532383239 -.7590387660 -.3617034846
+ 1.6803275058 .6775209988 -.5354837468 2.6208591363
+ 4.2086428525 3.9022731880 2.5001857370 2.5001857370
+
+ .4136122500 -.1637152873 .2212564728 2.1287126020
+ .3896388275 -.2354089650 2.3255326077 3.5388086279
+ 3.6078928145 2.1393094782 2.1393094782
+
+ -3.5193531074 -2.0157307929 1.8355926160 2.7489174124
+ 2.0098391558 1.7975718667 3.4209730327 3.0809713206
+ 1.4707077389 1.4707077389
+
+ -1.3532688232 2.5504275249 2.8202873790 1.6253609671
+ 1.8625091247 2.7995744193 3.0182595342 1.7373181916
+ 1.7373181916
+
+ 3.7292778697 2.2944436481 -.0303565255 3.1115776177
+ 4.8164268553 4.7935507272 3.1045342752 3.1045342752
+
+ -.0827362961 -1.6043113182 2.4439837435 3.8790755071
+ 3.8711928134 2.0152329038 2.0152329038
+
+ -4.3897783280 2.3664634533 3.5878262177 3.6826168780
+ 1.8196209136 1.8196209136
+
+ 4.1927969260 4.6457432555 4.4872661030 3.6395852546
+ 3.6395852546
+
+ 6.6296746680 6.6717260508 5.4858936024 5.4858936024
+
+ 6.6424306340 5.2914044780 5.2914044780
+
+ 4.3860654351 4.3860654351
+
+ 4.3860654351
+
& faceps1,faceps1_inv,eps1_om12,facsig,sigsq,sigsq_om1,sigsq_om2,
& sigsq_om12,facp,facp_inv,facp1,eps2rt,eps2rt_om1,eps2rt_om2,
& eps2rt_om12,eps3rt,eom1,eom2,eom12,evdwij,eps2der,eps3der,sigder,
- & dsci_inv,dscj_inv,gg
+ & dsci_inv,dscj_inv,gg,gg_lipi,gg_lipj
common /calc/ erij(3),rij,xj,yj,zj,dxi,dyi,dzi,dxj,dyj,dzj,
& chi1,chi2,chi12,chip1,chip2,chip12,alf1,alf2,alf12,om1,om2,om12,
& om1om2,chiom1,chiom2,chiom12,chipom1,chipom2,chipom12,eps1,
& faceps1,faceps1_inv,eps1_om12,facsig,sigsq,sigsq_om1,sigsq_om2,
& sigsq_om12,facp,facp_inv,facp1,eps2rt,eps2rt_om1,eps2rt_om2,
& eps2rt_om12,eps3rt,eom1,eom2,eom12,evdwij,eps2der,eps3der,sigder,
- & dsci_inv,dscj_inv,gg(3),i,j
+ & dsci_inv,dscj_inv,gg(3),gg_lipi(3),gg_lipj(3),i,j
integer nres,nsup,nstart_sup,nz_start,nz_end,iz_sc,
- & nres0,nstart_seq,chain_length,iprzes,tabperm,nperm
+ & nres0,nstart_seq,chain_length,iprzes,tabperm,nperm,afmend,
+ & afmbeg
double precision c,dc,dc_old,d_c_work,xloc,xrot,dc_norm,t,r,
- & prod,rt,dc_work,cref,crefjlee,chain_rep,dc_norm2
+ & prod,rt,dc_work,cref,crefjlee,chain_rep,dc_norm2,velAFMconst,
+ & totTafm
common /chain/ c(3,maxres2+2),dc(3,0:maxres2),dc_old(3,0:maxres2),
& xloc(3,maxres),xrot(3,maxres),dc_norm(3,0:maxres2),
& dc_norm2(3,0:maxres2),
& nsup,nstart_sup,nstart_seq,
& chain_length,iprzes,tabperm(maxperm,maxsym),nperm
common /from_zscore/ nz_start,nz_end,iz_sc
- double precision boxxsize,boxysize,boxzsize,enecut,sscut,sss,sssgrad
- common /box/ boxxsize,boxysize,boxzsize,enecut,sscut,sss,sssgrad
+ double precision boxxsize,boxysize,boxzsize,enecut,sscut,
+ & sss,sssgrad,
+ & buflipbot, bufliptop,bordlipbot,bordliptop,lipbufthick,lipthick
+ common /box/ boxxsize,boxysize,boxzsize,enecut,sscut,sss,sssgrad,
+ & buflipbot, bufliptop,bordlipbot,bordliptop,lipbufthick,lipthick
+ common /afm/ forceAFMconst, distafminit,afmend,afmbeg,
+ & velAFMconst,
+ & totTafm
+
integer modecalc,iscode,indpdb,indback,indphi,iranconf,icheckgrad,
- & inprint,i2ndstr,mucadyn,constr_dist,symetr
+ & inprint,i2ndstr,mucadyn,constr_dist,symetr,AFMlog,selfguide
logical minim,refstr,pdbref,outpdb,outmol2,overlapsc,energy_dec,
& sideadd,lsecondary,read_cart,unres_pdb,
& vdisulf,searchsc,lmuca,dccart,extconf,out1file,
& icheckgrad,minim,i2ndstr,refstr,pdbref,outpdb,outmol2,iprint,
& overlapsc,energy_dec,sideadd,lsecondary,read_cart,unres_pdb
& ,vdisulf,searchsc,lmuca,dccart,mucadyn,extconf,out1file,
- & constr_dist,gnorm_check,gradout,split_ene,symetr
+ & constr_dist,gnorm_check,gradout,split_ene,symetr,AFMlog,
+ & selfguide
C... minim = .true. means DO minimization.
C... energy_dec = .true. means print energy decomposition matrix
- double precision dcdv,dxdv,dxds,gradx,gradc,gvdwc,gelc,gelc_long,
- & gvdwpp,gel_loc,gel_loc_long,gvdwc_scpp,
+ double precision dcdv,dxdv,dxds,gradx,gradc,gvdwc,gelc,gelc_long
+ & gvdwpp,gel_loc,gel_loc_long,gvdwc_scpp,gliptranc,gliptranx,
& gradx_scp,gvdwc_scp,ghpbx,ghpbc,gloc,gloc_x,dtheta,dphi,dalpha,
& domega,gscloc,gsclocx,gradcorr,gradcorr_long,gradcorr5_long,
& gradcorr6_long,gcorr6_turn_long,gvdwx
integer nfl,icg
common /derivat/ dcdv(6,maxdim),dxdv(6,maxdim),dxds(6,maxres),
- & gradx(3,maxres,2),gradc(3,maxres,2),gvdwx(3,maxres),
- & gvdwc(3,maxres),gelc(3,maxres),gelc_long(3,maxres),
- & gvdwpp(3,maxres),gvdwc_scpp(3,maxres),
- & gradx_scp(3,maxres),gvdwc_scp(3,maxres),ghpbx(3,maxres),
- & ghpbc(3,maxres),gloc(0:maxvar,2),gradcorr(3,maxres),
- & gradcorr_long(3,maxres),gradcorr5_long(3,maxres),
- & gradcorr6_long(3,maxres),gcorr6_turn_long(3,maxres),
- & gradxorr(3,maxres),gradcorr5(3,maxres),gradcorr6(3,maxres),
- & gloc_x(maxvar,2),gel_loc(3,maxres),gel_loc_long(3,maxres),
- & gcorr3_turn(3,maxres),
- & gcorr4_turn(3,maxres),gcorr6_turn(3,maxres),gradb(3,maxres),
- & gradbx(3,maxres),gel_loc_loc(maxvar),gel_loc_turn3(maxvar),
- & gel_loc_turn4(maxvar),gel_loc_turn6(maxvar),gcorr_loc(maxvar),
- & g_corr5_loc(maxvar),g_corr6_loc(maxvar),gsccorc(3,maxres),
- & gsccorx(3,maxres),gsccor_loc(maxres),dtheta(3,2,maxres),
- & gscloc(3,maxres),gsclocx(3,maxres),
- & dphi(3,3,maxres),dalpha(3,3,maxres),domega(3,3,maxres),nfl,icg
+ & gradx(3,-1:maxres,2),gradc(3,-1:maxres,2),gvdwx(3,-1:maxres),
+ & gvdwc(3,-1:maxres),gelc(3,-1:maxres),gelc_long(3,-1:maxres),
+ & gvdwpp(3,-1:maxres),gvdwc_scpp(3,-1:maxres),
+ & gliptranc(3,-1:maxres),
+ & gliptranx(3,-1:maxres),
+ & gradafm(3,-1:maxres),
+ & gradx_scp(3,-1:maxres),gvdwc_scp(3,-1:maxres),
+ & ghpbx(3,-1:maxres),
+ & ghpbc(3,-1:maxres),gloc(maxvar,2),gradcorr(3,-1:maxres),
+ & gradcorr_long(3,-1:maxres),gradcorr5_long(3,-1:maxres),
+ & gradcorr6_long(3,-1:maxres),gcorr6_turn_long(3,-1:maxres),
+ & gradxorr(3,-1:maxres),gradcorr5(3,-1:maxres),
+ & gradcorr6(3,-1:maxres),
+ & gloc_x(maxvar,2),gel_loc(3,-1:maxres),gel_loc_long(3,-1:maxres),
+ & gcorr3_turn(3,-1:maxres),
+ & gcorr4_turn(3,-1:maxres),gcorr6_turn(3,-1:maxres),
+ & gradb(3,-1:maxres),
+ & gradbx(3,-1:maxres),gel_loc_loc(maxvar),gel_loc_turn3(maxvar),
+ & gel_loc_turn4(maxvar),gel_loc_turn6(maxvar),
+ & gcorr_loc(maxvar),
+ & g_corr5_loc(maxvar),g_corr6_loc(maxvar),gsccorc(3,-1:maxres),
+ & gsccorx(3,-1:maxres),gsccor_loc(-1:maxres),
+ & dtheta(3,2,-1:maxres),
+ & gscloc(3,-1:maxres),gsclocx(3,-1:maxres),
+ & dphi(3,3,-1:maxres),dalpha(3,3,-1:maxres),domega(3,3,-1:maxres),
+ & nfl,
+ & icg
double precision derx,derx_turn
common /deriv_loc/ derx(3,5,2),derx_turn(3,5,2)
double precision dXX_C1tab(3,maxres),dYY_C1tab(3,maxres),
integer n_ene_comp,rescale_mode
common /ffield/ wsc,wscp,welec,wbond,wstrain,wtor,wtor_d,wang,
& wscloc,wcorr,wcorr4,wcorr5,wcorr6,wsccor,wel_loc,wturn3,wturn4,
- & wturn6,wvdwpp,weights(n_ene),temp0,
+ & wturn6,wvdwpp,weights(n_ene),wliptran,temp0,
& scal14,cutoff_corr,delt_corr,r0_corr,ipot,n_ene_comp,
& rescale_mode
common /potentials/ potname(5)
- double precision aa,bb,augm,aad,bad,app,bpp,ale6,ael3,ael6
+ double precision aa,bb,augm,aad,bad,app,bpp,ale6,ael3,ael6,
+ &aa_lip,bb_lip,aa_aq,bb_aq
integer expon,expon2
integer nnt,nct,nint_gr,istart,iend,itype,itel,itypro,
& ielstart,ielend,ielstart_vdw,ielend_vdw,nscp_gr,iscpstart,
& iscpend,iatsc_s,iatsc_e,
& iatel_s,iatel_e,iatscp_s,iatscp_e,iatel_s_vdw,iatel_e_vdw,
& ispp,iscp
- common /interact/aa(ntyp,ntyp),bb(ntyp,ntyp),augm(ntyp,ntyp),
+ common /interact/aa_aq(ntyp,ntyp),bb_aq(ntyp,ntyp),
+ & aa_lip(ntyp,ntyp),bb_lip(ntyp,ntyp),
+ & augm(ntyp,ntyp),
& aad(ntyp,2),bad(ntyp,2),app(2,2),bpp(2,2),ael6(2,2),ael3(2,2),
& expon,expon2,nnt,nct,nint_gr(maxres),istart(maxres,maxint_gr),
& iend(maxres,maxint_gr),itype(maxres),itel(maxres),itypro,
& iatsc_s,iatsc_e,iatel_s,iatel_e,iatel_s_vdw,iatel_e_vdw,
& iatscp_s,iatscp_e,ispp,iscp
C 12/1/95 Array EPS included in the COMMON block.
- double precision eps,sigma,sigmaii,rs0,chi,chip,alp,sigma0,sigii,
+ double precision eps,epslip,sigma,sigmaii,rs0,chi,chip,alp,
+ & sigma0,sigii,
& rr0,r0,r0e,r0d,rpp,epp,elpp6,elpp3,eps_scp,rscp
- common /body/eps(ntyp,ntyp),sigma(0:ntyp1,0:ntyp1),
+ common /body/eps(ntyp,ntyp),epslip(ntyp,ntyp),
+ & sigma(0:ntyp1,0:ntyp1),
& sigmaii(ntyp,ntyp),
& rs0(ntyp,ntyp),chi(ntyp,ntyp),chip(ntyp),alp(ntyp),sigma0(ntyp),
& sigii(ntyp),rr0(ntyp),r0(ntyp,ntyp),r0e(ntyp,ntyp),r0d(ntyp,2),
& vbldsc0(maxbondterm,ntyp),akp,
& aksc(maxbondterm,ntyp),abond0(maxbondterm,ntyp),
& distchainmax,nbondterm(ntyp)
+C 01/29/15 Lipidic parameters
+ double precision pepliptran,liptranene
+ common /lipid/ pepliptran,liptranene(ntyp)
+
C Parameter files
character*256 bondname,thetname,rotname,torname,tordname,
& fouriername,elename,sidename,scpname,sccorname,patname,
- & thetname_pdb,rotname_pdb
+ & thetname_pdb,rotname_pdb,liptranname
common /parfiles/ bondname,thetname,rotname,torname,tordname,
& fouriername,elename,sidename,scpname,sccorname,patname,
- & thetname_pdb,rotname_pdb
+ & thetname_pdb,rotname_pdb,liptranname
character*3 pot
C-----------------------------------------------------------------------
C INP - main input file
& iphi_end,iphid_start,iphid_end,ibond_start,ibond_end,
& ibondp_start,ibondp_end,ivec_start,ivec_end,iset_start,iset_end,
& iturn3_start,iturn3_end,iturn4_start,iturn4_end,iint_start,
- & iint_end,iphi1_start,iphi1_end,itau_start,itau_end,
+ & iint_end,iphi1_start,iphi1_end,itau_start,itau_end,ilip_start,
+ & ilip_end,
& ibond_displ(0:max_fg_procs-1),ibond_count(0:max_fg_procs-1),
& ithet_displ(0:max_fg_procs-1),ithet_count(0:max_fg_procs-1),
& iphi_displ(0:max_fg_procs-1),iphi_count(0:max_fg_procs-1),
& iint_end,iphi1_start,iphi1_end,iint_count,iint_displ,ivec_displ,
& ivec_count,iset_displ,itau_start,itau_end,
& iset_count,ibond_displ,ibond_count,ithet_displ,ithet_count,
- & iphi_displ,iphi_count,iphi1_displ,iphi1_count
+ & iphi_displ,iphi_count,iphi1_displ,iphi1_count,ilip_start,ilip_end
C Inverses of the actual virtual bond lengths
common /invlen/ vbld_inv(maxres2)
& nlor_sccor(-ntyp:ntyp,-ntyp:ntyp),
& vlor1sccor(maxterm_sccor,20,20),
& vlor2sccor(maxterm_sccor,20,20),
- & vlor3sccor(maxterm_sccor,20,20),gloc_sc(3,0:maxres2,10),
+ & vlor3sccor(maxterm_sccor,20,20),gloc_sc(3,-1:maxres2,10),
& dcostau(3,3,3,maxres2),dsintau(3,3,3,maxres2),
& dtauangle(3,3,3,maxres2),dcosomicron(3,3,3,maxres2),
& domicron(3,3,3,maxres2)
********************************************************************************
C Max. number of processors.
integer maxprocs
- parameter (maxprocs=2048)
+ parameter (maxprocs=1028)
C Max. number of fine-grain processors
integer max_fg_procs
c parameter (max_fg_procs=maxprocs)
- parameter (max_fg_procs=512)
+ parameter (max_fg_procs=256)
C Max. number of coarse-grain processors
integer max_cg_procs
parameter (max_cg_procs=maxprocs)
C Max. number of AA residues
integer maxres
- parameter (maxres=800)
+ parameter (maxres=600)
C Appr. max. number of interaction sites
integer maxres2,maxres6,mmaxres2
parameter (maxres2=2*maxres,maxres6=6*maxres)
parameter (max_pool=10)
C Number of energy components
integer n_ene,n_ene2
- parameter (n_ene=21,n_ene2=2*n_ene)
+ parameter (n_ene=23,n_ene2=2*n_ene)
C Number of threads in deformation
integer max_thread,max_thread2
parameter (max_thread=4,max_thread2=2*max_thread)
#endif
endif
if (ntwe.ne.0) then
- if (mod(itime,ntwe).eq.0) call statout(itime)
+ if (mod(itime,ntwe).eq.0) then
+ call statout(itime)
+C call enerprint(potEcomp)
+C print *,itime,'AFM',Eafmforc,etot
+ endif
#ifdef VOUT
do j=1,3
v_work(j)=d_t(j,0)
#endif
endif
if (mod(itime,ntwx).eq.0) then
+ write(iout,*) 'time=',itime
+C call check_ecartint
call returnbox
write (tytul,'("time",f8.2)') totT
if(mdpdb) then
endif
if (rattle) call rattle2
totT=totT+d_time
+ totTafm=totT
+C print *,totTafm,"TU?"
if (d_time.ne.d_time0) then
d_time=d_time0
#ifndef LANG0
potE=potEcomp(0)-potEcomp(20)
c potE=energia_short(0)+energia_long(0)
totT=totT+d_time
+ totTafm=totT
c Calculate the kinetic and the total energy and the kinetic temperature
call kinetic(EK)
totE=EK+potE
d_t(j,0)=d_t_old(j,0)+adt
enddo
do i=nnt,nct-1
+C SPYTAC ADAMA
+C do i=0,nres
do j=1,3
adt=d_a_old(j,i)*d_time
adt2=0.5d0*adt
enddo
enddo
do i=nnt,nct
+C do i=0,nres
if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
endif
call random_vel
totT=0.0d0
+ totTafm=totT
endif
else
c Generate initial velocities
& write(iout,*) "Initial velocities randomly generated"
call random_vel
totT=0.0d0
+CtotTafm is the variable for AFM time which eclipsed during
+ totTafm=totT
endif
c rest2name = prefix(:ilen(prefix))//'.rst'
if(me.eq.king.or..not.out1file)then
include 'COMMON.IOUNITS'
include 'COMMON.NAMES'
include 'COMMON.TIME1'
- double precision xv,sigv,lowb,highb
+ double precision xv,sigv,lowb,highb,vec_afm(3)
c Generate random velocities from Gaussian distribution of mean 0 and std of KT/m
c First generate velocities in the eigenspace of the G matrix
c write (iout,*) "Calling random_vel dimen dimen3",dimen,dimen3
lowb=-5*sigv
highb=5*sigv
d_t_work_new(ii)=anorm_distr(xv,sigv,lowb,highb)
+
c write (iout,*) "i",i," ii",ii," geigen",geigen(i),
c & " d_t_work_new",d_t_work_new(ii)
enddo
enddo
+C if (SELFGUIDE.gt.0) then
+C distance=0.0
+C do j=1,3
+C vec_afm(j)=c(j,afmend)-c(j,afmbeg)
+C distance=distance+vec_afm(j)**2
+C enddo
+C distance=dsqrt(distance)
+C do j=1,3
+C d_t_work_new(j+(afmbeg-1)*3)=-velAFMconst*vec_afm(j)/distance
+C d_t_work_new(j+(afmend-1)*3)=velAFMconst*vec_afm(j)/distance
+C write(iout,*) "myvel",d_t_work_new(j+(afmbeg-1)*3),
+C & d_t_work_new(j+(afmend-1)*3)
+C enddo
+
+C endif
+
c diagnostics
c Ek1=0.0d0
c ii=0
if(me.eq.king) close(irest2)
return
end
+c------------------------------------------
potE=potEcomp(0)-potEcomp(20)
call cartgrad
totT=totT+d_time
+ totTafm=totT
c Calculate the kinetic and total energy and the kinetic temperature
call kinetic(EK)
#ifdef MPI
perbox=.false.
fail=.false.
print *, 'enter chainbuild'
+ call chainbuild_cart
+ return
+ end
+#ifdef DEBUG
if (perbox) then
cost=dcos(theta(3))
sint=dsin(theta(3))
endif
return
end
+#endif
c-------------------------------------------------------------------------
subroutine orig_frame
C
c write(iout,'(2i5,2(a,f15.10))')i,j," etot",etot," etot1",etot1
dc(j,i)=ddc(j)-aincr
call chainbuild_cart
+C print *,c(j,i)
c call int_from_cart1(.false.)
if (.not.split_ene) then
call etotal(energia1(0))
C-----------------------------------------------------------------------
+ double precision function sscalelip(r)
+ double precision r,gamm
+ include "COMMON.SPLITELE"
+C if(r.lt.r_cut-rlamb) then
+C sscale=1.0d0
+C else if(r.le.r_cut.and.r.ge.r_cut-rlamb) then
+C gamm=(r-(r_cut-rlamb))/rlamb
+ sscalelip=1.0d0+r*r*(2*r-3.0d0)
+C else
+C sscale=0d0
+C endif
+ return
+ end
+C-----------------------------------------------------------------------
+ double precision function sscagradlip(r)
+ double precision r,gamm
+ include "COMMON.SPLITELE"
+C if(r.lt.r_cut-rlamb) then
+C sscagrad=0.0d0
+C else if(r.le.r_cut.and.r.ge.r_cut-rlamb) then
+C gamm=(r-(r_cut-rlamb))/rlamb
+ sscagradlip=r*(6*r-6.0d0)
+C else
+C sscagrad=0.0d0
+C endif
+ return
+ end
+
+C-----------------------------------------------------------------------
double precision function sscale(r)
double precision r,gamm
include "COMMON.SPLITELE"
rrij=1.0D0/rij
eps0ij=eps(itypi,itypj)
fac=rrij**expon2
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=e1+e2
evdw=evdw+(1.0d0-sss)*evdwij
C
rrij=1.0D0/rij
eps0ij=eps(itypi,itypj)
fac=rrij**expon2
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=e1+e2
evdw=evdw+sss*evdwij
C
if (sss.lt.1.0d0) then
r_shift_inv=1.0D0/(rij+r0(itypi,itypj)-sigma(itypi,itypj))
fac=r_shift_inv**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=e_augm+e1+e2
cd sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
cd epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
if (sss.gt.0.0d0) then
r_shift_inv=1.0D0/(rij+r0(itypi,itypj)-sigma(itypi,itypj))
fac=r_shift_inv**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=e_augm+e1+e2
cd sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
cd epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
C Calculate whole angle-dependent part of epsilon and contributions
C to its derivatives
fac=(rrij*sigsq)**expon2
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+evdwij*(1.0d0-sss)
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa
cd write (iout,'(2(a3,i3,2x),15(0pf7.3))')
cd & restyp(itypi),i,restyp(itypj),j,
cd & epsi,sigm,chi1,chi2,chip1,chip2,
C Calculate whole angle-dependent part of epsilon and contributions
C to its derivatives
fac=(rrij*sigsq)**expon2
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+evdwij*sss
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa
cd write (iout,'(2(a3,i3,2x),15(0pf7.3))')
cd & restyp(itypi),i,restyp(itypj),j,
cd & epsi,sigm,chi1,chi2,chip1,chip2,
if (yj.lt.0) yj=yj+boxysize
zj=mod(zj,boxzsize)
if (zj.lt.0) zj=zj+boxzsize
+ if ((zj.gt.bordlipbot)
+ &.and.(zj.lt.bordliptop)) then
+C the energy transfer exist
+ if (zj.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((positi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick)
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipj=1.0d0
+ ssgradlipj=0.0
+ endif
+ else
+ sslipj=0.0d0
+ ssgradlipj=0.0
+ endif
+ aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +aa_aq(itypi,itypj)*(2.0d0-sslipi+sslipj)/2.0d0
+ bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +bb_aq(itypi,itypj)*(2.0d0-sslipi+sslipj)/2.0d0
+
dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
xj_safe=xj
yj_safe=yj
c---------------------------------------------------------------
rij_shift=1.0D0/rij_shift
fac=rij_shift**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+evdwij*(1.0d0-sss)
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa
write (iout,'(2(a3,i3,2x),17(0pf7.3))')
& restyp(itypi),i,restyp(itypj),j,
& epsi,sigm,chi1,chi2,chip1,chip2,
gg(1)=xj*fac
gg(2)=yj*fac
gg(3)=zj*fac
+ gg_lipi(3)=ssgradlipi*evdwij
+ gg_lipj(3)=ssgradlipj*evdwij
C Calculate angular part of the gradient.
call sc_grad_scale(1.0d0-sss)
endif
if (yj.lt.0) yj=yj+boxysize
zj=mod(zj,boxzsize)
if (zj.lt.0) zj=zj+boxzsize
+ if ((zj.gt.bordlipbot)
+ &.and.(zj.lt.bordliptop)) then
+C the energy transfer exist
+ if (zj.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((positi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick)
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipj=1.0d0
+ ssgradlipj=0.0
+ endif
+ else
+ sslipj=0.0d0
+ ssgradlipj=0.0
+ endif
+ aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +aa_aq(itypi,itypj)*(2.0d0-sslipi+sslipj)/2.0d0
+ bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +bb_aq(itypi,itypj)*(2.0d0-sslipi+sslipj)/2.0d0
dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
xj_safe=xj
yj_safe=yj
c---------------------------------------------------------------
rij_shift=1.0D0/rij_shift
fac=rij_shift**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+evdwij*sss
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa
write (iout,'(2(a3,i3,2x),17(0pf7.3))')
& restyp(itypi),i,restyp(itypj),j,
& epsi,sigm,chi1,chi2,chip1,chip2,
gg(1)=xj*fac
gg(2)=yj*fac
gg(3)=zj*fac
+ gg_lipi(3)=ssgradlipi*evdwij
+ gg_lipj(3)=ssgradlipj*evdwij
C Calculate angular part of the gradient.
call sc_grad_scale(sss)
endif
c---------------------------------------------------------------
rij_shift=1.0D0/rij_shift
fac=rij_shift**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+(evdwij+e_augm)*(1.0d0-sss)
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa
write (iout,'(2(a3,i3,2x),17(0pf7.3))')
& restyp(itypi),i,restyp(itypj),j,
& epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),
c---------------------------------------------------------------
rij_shift=1.0D0/rij_shift
fac=rij_shift**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+(evdwij+e_augm)*sss
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa
write (iout,'(2(a3,i3,2x),17(0pf7.3))')
& restyp(itypi),i,restyp(itypj),j,
& epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),
enddo
c write (iout,*) "gg",(gg(k),k=1,3)
do k=1,3
- gvdwx(k,i)=gvdwx(k,i)-gg(k)
+ gvdwx(k,i)=gvdwx(k,i)-gg(k)+gg_lipi(k)
& +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))
& +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv*scalfac
- gvdwx(k,j)=gvdwx(k,j)+gg(k)
+ gvdwx(k,j)=gvdwx(k,j)+gg(k)+gg_lipj(k)
& +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j))
& +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv*scalfac
c write (iout,*)(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))
C Calculate the components of the gradient in DC and X
C
do l=1,3
- gvdwc(l,i)=gvdwc(l,i)-gg(l)
- gvdwc(l,j)=gvdwc(l,j)+gg(l)
+ gvdwc(l,i)=gvdwc(l,i)-gg(l)+gg_lipi(k)
+ gvdwc(l,j)=gvdwc(l,j)+gg(l)+gg_lipj(k)
enddo
return
end
C
C Compute the side-chain and electrostatic interaction energy
C
+C print *,ipot
goto (101,102,103,104,105,106) ipot
C Lennard-Jones potential.
101 call elj(evdw)
goto 107
C Gay-Berne potential (shifted LJ, angular dependence).
104 call egb(evdw)
+C print *,"bylem w egb"
goto 107
C Gay-Berne-Vorobjev potential (shifted LJ, angular dependence).
105 call egbv(evdw)
C
C Calculate the SC local energy.
C
+C print *,"TU DOCHODZE?"
call esc(escloc)
c print *,"Processor",myrank," computed USC"
C
else
esccor=0.0d0
endif
+C print *,"PRZED MULIt"
c print *,"Processor",myrank," computed Usccorr"
C
C 12/1/95 Multi-body terms
Uconst=0.0d0
Uconst_back=0.0d0
endif
+C 01/27/2015 added by adasko
+C the energy component below is energy transfer into lipid environment
+C based on partition function
+C print *,"przed lipidami"
+ if (wliptran.gt.0) then
+ call Eliptransfer(eliptran)
+ endif
+C print *,"za lipidami"
+ if (AFMlog.gt.0) then
+ call AFMforce(Eafmforce)
+ else if (selfguide.gt.0) then
+ call AFMvel(Eafmforce)
+ endif
#ifdef TIMING
time_enecalc=time_enecalc+MPI_Wtime()-time00
#endif
energia(17)=estr
energia(20)=Uconst+Uconst_back
energia(21)=esccor
+ energia(22)=eliptran
+ energia(23)=Eafmforce
c Here are the energies showed per procesor if the are more processors
c per molecule then we sum it up in sum_energy subroutine
c print *," Processor",myrank," calls SUM_ENERGY"
estr=energia(17)
Uconst=energia(20)
esccor=energia(21)
+ eliptran=energia(22)
+ Eafmforce=energia(23)
#ifdef SPLITELE
etot=wsc*evdw+wscp*evdw2+welec*ees+wvdwpp*evdw1
& +wang*ebe+wtor*etors+wscloc*escloc
& +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5
& +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3
& +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d
- & +wbond*estr+Uconst+wsccor*esccor
+ & +wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran+Eafmforce
#else
etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1)
& +wang*ebe+wtor*etors+wscloc*escloc
& +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5
& +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3
& +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d
- & +wbond*estr+Uconst+wsccor*esccor
+ & +wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran
+ & +Eafmforce
#endif
energia(0)=etot
c detecting NaNQ
#ifdef MPI
include 'mpif.h'
#endif
- double precision gradbufc(3,maxres),gradbufx(3,maxres),
- & glocbuf(4*maxres),gradbufc_sum(3,maxres),gloc_scbuf(3,maxres)
+ double precision gradbufc(3,-1:maxres),gradbufx(3,-1:maxres),
+ & glocbuf(4*maxres),gradbufc_sum(3,-1:maxres)
+ & ,gloc_scbuf(3,-1:maxres)
include 'COMMON.SETUP'
include 'COMMON.IOUNITS'
include 'COMMON.FFIELD'
call flush(iout)
#endif
#ifdef SPLITELE
- do i=1,nct
+ do i=0,nct
do j=1,3
gradbufc(j,i)=wsc*gvdwc(j,i)+
& wscp*(gvdwc_scp(j,i)+gvdwc_scpp(j,i))+
& wcorr6*gradcorr6_long(j,i)+
& wturn6*gcorr6_turn_long(j,i)+
& wstrain*ghpbc(j,i)
+ & +wliptran*gliptranc(j,i)
+ & +gradafm(j,i)
+
enddo
enddo
#else
- do i=1,nct
+ do i=0,nct
do j=1,3
gradbufc(j,i)=wsc*gvdwc(j,i)+
& wscp*(gvdwc_scp(j,i)+gvdwc_scpp(j,i))+
& wcorr6*gradcorr6_long(j,i)+
& wturn6*gcorr6_turn_long(j,i)+
& wstrain*ghpbc(j,i)
+ & +wliptran*gliptranc(j,i)
+ & +gradafm(j,i)
+
enddo
enddo
#endif
enddo
call flush(iout)
#endif
- do i=1,nres
+ do i=0,nres
do j=1,3
gradbufc_sum(j,i)=gradbufc(j,i)
enddo
do j=1,3
gradbufc(j,nres-1)=gradbufc_sum(j,nres)
enddo
- do i=nres-2,nnt,-1
+ do i=nres-2,-1,-1
do j=1,3
gradbufc(j,i)=gradbufc(j,i+1)+gradbufc_sum(j,i+1)
enddo
enddo
call flush(iout)
#endif
- do i=1,nres
+ do i=-1,nres
do j=1,3
gradbufc_sum(j,i)=gradbufc(j,i)
gradbufc(j,i)=0.0d0
do j=1,3
gradbufc(j,nres-1)=gradbufc_sum(j,nres)
enddo
- do i=nres-2,nnt,-1
+ do i=nres-2,-1,-1
do j=1,3
gradbufc(j,i)=gradbufc(j,i+1)+gradbufc_sum(j,i+1)
enddo
do k=1,3
gradbufc(k,nres)=0.0d0
enddo
- do i=1,nct
+ do i=-1,nct
do j=1,3
#ifdef SPLITELE
gradc(j,i,icg)=gradbufc(j,i)+welec*gelc(j,i)+
& wturn6*gcorr6_turn(j,i)+
& wsccor*gsccorc(j,i)
& +wscloc*gscloc(j,i)
+ & +wliptran*gliptranc(j,i)
+ & +gradafm(j,i)
#else
gradc(j,i,icg)=gradbufc(j,i)+welec*gelc(j,i)+
& wel_loc*gel_loc(j,i)+
& wturn6*gcorr6_turn(j,i)+
& wsccor*gsccorc(j,i)
& +wscloc*gscloc(j,i)
+ & +wliptran*gliptranc(j,i)
+ & +gradafm(j,i)
+
#endif
gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+
& wbond*gradbx(j,i)+
& wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+
& wsccor*gsccorx(j,i)
& +wscloc*gsclocx(j,i)
+ & +wliptran*gliptranx(j,i)
enddo
enddo
#ifdef DEBUG
estr=energia(17)
Uconst=energia(20)
esccor=energia(21)
+ eliptran=energia(22)
+ Eafmforce=energia(23)
#ifdef SPLITELE
write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,evdw1,wvdwpp,
& estr,wbond,ebe,wang,
& ecorr5,wcorr5,ecorr6,wcorr6,eel_loc,wel_loc,eello_turn3,wturn3,
& eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccor,
& edihcnstr,ebr*nss,
- & Uconst,etot
+ & Uconst,eliptran,wliptran,Eafmforce,etot
10 format (/'Virtual-chain energies:'//
& 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/
& 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/
& 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/
& 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/
& 'UCONST= ',1pE16.6,' (Constraint energy)'/
+ & 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/
+ & 'EAFM= ',1pE16.6,' (atomic-force microscopy)'/
& 'ETOT= ',1pE16.6,' (total)')
+
#else
write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,
& estr,wbond,ebe,wang,
& ecorr,wcorr,
& ecorr5,wcorr5,ecorr6,wcorr6,eel_loc,wel_loc,eello_turn3,wturn3,
& eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccro,edihcnstr,
- & ebr*nss,Uconst,etot
+ & ebr*nss,Uconst,eliptran,wliptran,Eafmforc,etot
10 format (/'Virtual-chain energies:'//
& 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/
& 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/
& 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/
& 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/
& 'UCONST=',1pE16.6,' (Constraint energy)'/
+ & 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/
+ & 'EAFM= ',1pE16.6,' (atomic-force microscopy)'/
& 'ETOT= ',1pE16.6,' (total)')
#endif
return
c write (iout,*)'i=',i,' j=',j,' itypi=',itypi,' itypj=',itypj
eps0ij=eps(itypi,itypj)
fac=rrij**expon2
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+C have you changed here?
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=e1+e2
cd sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
cd epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
cd write (iout,'(2(a3,i3,2x),6(1pd12.4)/2(3(1pd12.4),5x)/)')
-cd & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj),
+cd & restyp(itypi),i,restyp(itypj),j,a(itypi,itypj),
cd & bb(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,epsi,sigm,
cd & (c(k,i),k=1,3),(c(k,j),k=1,3)
evdw=evdw+evdwij
rij=1.0D0/r_inv_ij
r_shift_inv=1.0D0/(rij+r0(itypi,itypj)-sigma(itypi,itypj))
fac=r_shift_inv**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+C have you changed here?
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=e_augm+e1+e2
cd sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
cd epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
call sc_angular
C Calculate whole angle-dependent part of epsilon and contributions
C to its derivatives
+C have you changed here?
fac=(rrij*sigsq)**expon2
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+evdwij
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa
cd write (iout,'(2(a3,i3,2x),15(0pf7.3))')
cd & restyp(itypi),i,restyp(itypj),j,
cd & epsi,sigm,chi1,chi2,chip1,chip2,
integer xshift,yshift,zshift
evdw=0.0D0
ccccc energy_dec=.false.
-c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
+C print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
lprn=.false.
c if (icall.eq.0) lprn=.false.
if (yi.lt.0) yi=yi+boxysize
zi=mod(zi,boxzsize)
if (zi.lt.0) zi=zi+boxzsize
+C define scaling factor for lipids
+
+C if (positi.le.0) positi=positi+boxzsize
+C print *,i
+C first for peptide groups
+c for each residue check if it is in lipid or lipid water border area
+ if ((zi.gt.bordlipbot)
+ &.and.(zi.lt.bordliptop)) then
+C the energy transfer exist
+ if (zi.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick)
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipi=1.0d0
+ ssgradlipi=0.0
+ endif
+ else
+ sslipi=0.0d0
+ ssgradlipi=0.0
+ endif
+
C xi=xi+xshift*boxxsize
C yi=yi+yshift*boxysize
C zi=zi+zshift*boxzsize
if (yj.lt.0) yj=yj+boxysize
zj=mod(zj,boxzsize)
if (zj.lt.0) zj=zj+boxzsize
+ if ((zj.gt.bordlipbot)
+ &.and.(zj.lt.bordliptop)) then
+C the energy transfer exist
+ if (zj.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zj-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zj.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipj=1.0d0
+ ssgradlipj=0.0
+ endif
+ else
+ sslipj=0.0d0
+ ssgradlipj=0.0
+ endif
+ aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+ bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+C if (aa.ne.aa_aq(itypi,itypj)) write(63,'(2e10.5)')
+C &(aa-aa_aq(itypi,itypj)),(bb-bb_aq(itypi,itypj))
+C if (ssgradlipj.gt.0.0d0) print *,"??WTF??"
+C print *,sslipi,sslipj,bordlipbot,zi,zj
dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
xj_safe=xj
yj_safe=yj
c---------------------------------------------------------------
rij_shift=1.0D0/rij_shift
fac=rij_shift**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+C here to start with
+C if (c(i,3).gt.
+ faclip=fac
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
+C write(63,'(2i3,2e10.3,2f10.5)') i,j,aa,bb, evdwij,
+C &((sslipi+sslipj)/2.0d0+
+C &(2.0d0-sslipi-sslipj)/2.0d0)
c write (iout,*) "sigsq",sigsq," sig",sig," eps2rt",eps2rt,
c & " eps3rt",eps3rt," eps1",eps1," e1",e1," e2",e2
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+evdwij*sss
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa
write (iout,'(2(a3,i3,2x),17(0pf7.3))')
& restyp(itypi),i,restyp(itypj),j,
& epsi,sigm,chi1,chi2,chip1,chip2,
fac=fac+evdwij/sss*sssgrad/sigma(itypi,itypj)*rij
c fac=0.0d0
C Calculate the radial part of the gradient
+ gg_lipi(3)=eps1*(eps2rt*eps2rt)
+ &*(eps3rt*eps3rt)*sss/2.0d0*(faclip*faclip*
+ & (aa_lip(itypi,itypj)-aa_aq(itypi,itypj))
+ &+faclip*(bb_lip(itypi,itypj)-bb_aq(itypi,itypj)))
+ gg_lipj(3)=ssgradlipj*gg_lipi(3)
+ gg_lipi(3)=gg_lipi(3)*ssgradlipi
+C gg_lipi(3)=0.0d0
+C gg_lipj(3)=0.0d0
gg(1)=xj*fac
gg(2)=yj*fac
gg(3)=zj*fac
C Calculate angular part of the gradient.
call sc_grad
- endif ! sss
+ endif
ENDIF ! dyn_ss
enddo ! j
enddo ! iint
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
+ xi=mod(xi,boxxsize)
+ if (xi.lt.0) xi=xi+boxxsize
+ yi=mod(yi,boxysize)
+ if (yi.lt.0) yi=yi+boxysize
+ zi=mod(zi,boxzsize)
+ if (zi.lt.0) zi=zi+boxzsize
+C define scaling factor for lipids
+
+C if (positi.le.0) positi=positi+boxzsize
+C print *,i
+C first for peptide groups
+c for each residue check if it is in lipid or lipid water border area
+ if ((zi.gt.bordlipbot)
+ &.and.(zi.lt.bordliptop)) then
+C the energy transfer exist
+ if (zi.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick)
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipi=1.0d0
+ ssgradlipi=0.0
+ endif
+ else
+ sslipi=0.0d0
+ ssgradlipi=0.0
+ endif
+
dxi=dc_norm(1,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
c alf1=0.0D0
c alf2=0.0D0
c alf12=0.0D0
- xj=c(1,nres+j)-xi
- yj=c(2,nres+j)-yi
- zj=c(3,nres+j)-zi
+C xj=c(1,nres+j)-xi
+C yj=c(2,nres+j)-yi
+C zj=c(3,nres+j)-zi
+ xj=mod(xj,boxxsize)
+ if (xj.lt.0) xj=xj+boxxsize
+ yj=mod(yj,boxysize)
+ if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+ if ((zj.gt.bordlipbot)
+ &.and.(zj.lt.bordliptop)) then
+C the energy transfer exist
+ if (zj.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zj-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zj.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipj=1.0d0
+ ssgradlipj=0.0
+ endif
+ else
+ sslipj=0.0d0
+ ssgradlipj=0.0
+ endif
+ aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+ bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+C if (aa.ne.aa_aq(itypi,itypj)) write(63,'2e10.5')
+C &(aa-aa_aq(itypi,itypj)),(bb-bb_aq(itypi,itypj))
+ dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ xj_safe=xj
+ yj_safe=yj
+ zj_safe=zj
+ subchap=0
+ do xshift=-1,1
+ do yshift=-1,1
+ do zshift=-1,1
+ xj=xj_safe+xshift*boxxsize
+ yj=yj_safe+yshift*boxysize
+ zj=zj_safe+zshift*boxzsize
+ dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ if(dist_temp.lt.dist_init) then
+ dist_init=dist_temp
+ xj_temp=xj
+ yj_temp=yj
+ zj_temp=zj
+ subchap=1
+ endif
+ enddo
+ enddo
+ enddo
+ if (subchap.eq.1) then
+ xj=xj_temp-xi
+ yj=yj_temp-yi
+ zj=zj_temp-zi
+ else
+ xj=xj_safe-xi
+ yj=yj_safe-yi
+ zj=zj_safe-zi
+ endif
dxj=dc_norm(1,nres+j)
dyj=dc_norm(2,nres+j)
dzj=dc_norm(3,nres+j)
c---------------------------------------------------------------
rij_shift=1.0D0/rij_shift
fac=rij_shift**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+evdwij+e_augm
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa
write (iout,'(2(a3,i3,2x),17(0pf7.3))')
& restyp(itypi),i,restyp(itypj),j,
& epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),
fac=-expon*(e1+evdwij)*rij_shift
sigder=fac*sigder
fac=rij*fac-2*expon*rrij*e_augm
+ fac=fac+evdwij/sss*sssgrad/sigma(itypi,itypj)*rij
C Calculate the radial part of the gradient
gg(1)=xj*fac
gg(2)=yj*fac
enddo
c write (iout,*) "gg",(gg(k),k=1,3)
do k=1,3
- gvdwx(k,i)=gvdwx(k,i)-gg(k)
+ gvdwx(k,i)=gvdwx(k,i)-gg(k)+gg_lipi(k)
& +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))
& +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv*sss
- gvdwx(k,j)=gvdwx(k,j)+gg(k)
+ gvdwx(k,j)=gvdwx(k,j)+gg(k)+gg_lipj(k)
& +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j))
& +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv*sss
c write (iout,*)(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))
cgrad enddo
cgrad enddo
do l=1,3
- gvdwc(l,i)=gvdwc(l,i)-gg(l)
- gvdwc(l,j)=gvdwc(l,j)+gg(l)
+ gvdwc(l,i)=gvdwc(l,i)-gg(l)+gg_lipi(l)
+ gvdwc(l,j)=gvdwc(l,j)+gg(l)+gg_lipj(l)
enddo
return
end
C
C 14/01/2014 TURN3,TUNR4 does no go under periodic boundry condition
do i=iturn3_start,iturn3_end
+ if (i.le.1) cycle
+C write(iout,*) "tu jest i",i
if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
C changes suggested by Ana to avoid out of bounds
& .or.((i+4).gt.nres)
num_cont_hb(i)=num_conti
enddo
do i=iturn4_start,iturn4_end
+ if (i.le.1) cycle
if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
C changes suggested by Ana to avoid out of bounds
& .or.((i+5).gt.nres)
c Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3
c
do i=iatel_s,iatel_e
+ if (i.le.1) cycle
if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
C changes suggested by Ana to avoid out of bounds
& .or.((i+2).gt.nres)
c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
num_conti=num_cont_hb(i)
do j=ielstart(i),ielend(i)
-c write (iout,*) i,j,itype(i),itype(j)
+C write (iout,*) i,j
+ if (j.le.1) cycle
if (itype(j).eq.ntyp1.or. itype(j+1).eq.ntyp1
C changes suggested by Ana to avoid out of bounds
& .or.((j+2).gt.nres)
c & dhpb(i),dhpb1(i),forcon(i)
C 24/11/03 AL: SS bridges handled separately because of introducing a specific
C distance and angle dependent SS bond potential.
- if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
- & iabs(itype(jjj)).eq.1) then
+C if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+C & iabs(itype(jjj)).eq.1) then
cmc if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
C 18/07/06 MC: Use the convention that the first nss pairs are SS bonds
if (.not.dyn_ss .and. i.le.nss) then
ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
enddo
endif
- endif
enddo
ehpb=0.5D0*ehpb
return
return
end
+CCC----------------------------------------------
+ subroutine Eliptransfer(eliptran)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CALC'
+ include 'COMMON.CONTROL'
+ include 'COMMON.SPLITELE'
+ include 'COMMON.SBRIDGE'
+C this is done by Adasko
+C print *,"wchodze"
+C structure of box:
+C water
+C--bordliptop-- buffore starts
+C--bufliptop--- here true lipid starts
+C lipid
+C--buflipbot--- lipid ends buffore starts
+C--bordlipbot--buffore ends
+ eliptran=0.0
+ do i=ilip_start,ilip_end
+C do i=1,1
+ if (itype(i).eq.ntyp1) cycle
+
+ positi=(mod(((c(3,i)+c(3,i+1))/2.0d0),boxzsize))
+ if (positi.le.0) positi=positi+boxzsize
+C print *,i
+C first for peptide groups
+c for each residue check if it is in lipid or lipid water border area
+ if ((positi.gt.bordlipbot)
+ &.and.(positi.lt.bordliptop)) then
+C the energy transfer exist
+ if (positi.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((positi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=-sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*pepliptran
+ gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0
+ gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0
+C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran
+
+C print *,"doing sccale for lower part"
+C print *,i,sslip,fracinbuf,ssgradlip
+ elseif (positi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick)
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*pepliptran
+ gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0
+ gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0
+C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran
+C print *, "doing sscalefor top part"
+C print *,i,sslip,fracinbuf,ssgradlip
+ else
+ eliptran=eliptran+pepliptran
+C print *,"I am in true lipid"
+ endif
+C else
+C eliptran=elpitran+0.0 ! I am in water
+ endif
+ enddo
+C print *, "nic nie bylo w lipidzie?"
+C now multiply all by the peptide group transfer factor
+C eliptran=eliptran*pepliptran
+C now the same for side chains
+CV do i=1,1
+ do i=ilip_start,ilip_end
+ if (itype(i).eq.ntyp1) cycle
+ positi=(mod(c(3,i+nres),boxzsize))
+ if (positi.le.0) positi=positi+boxzsize
+C print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop
+c for each residue check if it is in lipid or lipid water border area
+C respos=mod(c(3,i+nres),boxzsize)
+C print *,positi,bordlipbot,buflipbot
+ if ((positi.gt.bordlipbot)
+ & .and.(positi.lt.bordliptop)) then
+C the energy transfer exist
+ if (positi.lt.buflipbot) then
+ fracinbuf=1.0d0-
+ & ((positi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=-sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*liptranene(itype(i))
+ gliptranx(3,i)=gliptranx(3,i)
+ &+ssgradlip*liptranene(itype(i))
+ gliptranc(3,i-1)= gliptranc(3,i-1)
+ &+ssgradlip*liptranene(itype(i))
+C print *,"doing sccale for lower part"
+ elseif (positi.gt.bufliptop) then
+ fracinbuf=1.0d0-
+ &((bordliptop-positi)/lipbufthick)
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*liptranene(itype(i))
+ gliptranx(3,i)=gliptranx(3,i)
+ &+ssgradlip*liptranene(itype(i))
+ gliptranc(3,i-1)= gliptranc(3,i-1)
+ &+ssgradlip*liptranene(itype(i))
+C print *, "doing sscalefor top part",sslip,fracinbuf
+ else
+ eliptran=eliptran+liptranene(itype(i))
+C print *,"I am in true lipid"
+ endif
+ endif ! if in lipid or buffor
+C else
+C eliptran=elpitran+0.0 ! I am in water
+ enddo
+ return
+ end
+C---------------------------------------------------------
+C AFM soubroutine for constant force
+ subroutine AFMforce(Eafmforce)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CALC'
+ include 'COMMON.CONTROL'
+ include 'COMMON.SPLITELE'
+ include 'COMMON.SBRIDGE'
+ real*8 diffafm(3)
+ dist=0.0d0
+ Eafmforce=0.0d0
+ do i=1,3
+ diffafm(i)=c(i,afmend)-c(i,afmbeg)
+ dist=dist+diffafm(i)**2
+ enddo
+ dist=dsqrt(dist)
+ Eafmforce=-forceAFMconst*(dist-distafminit)
+ do i=1,3
+ gradafm(i,afmend-1)=-forceAFMconst*diffafm(i)/dist
+ gradafm(i,afmbeg-1)=forceAFMconst*diffafm(i)/dist
+ enddo
+C print *,'AFM',Eafmforce
+ return
+ end
+C---------------------------------------------------------
+C AFM subroutine with pseudoconstant velocity
+ subroutine AFMvel(Eafmforce)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CALC'
+ include 'COMMON.CONTROL'
+ include 'COMMON.SPLITELE'
+ include 'COMMON.SBRIDGE'
+ real*8 diffafm(3)
+C Only for check grad COMMENT if not used for checkgrad
+C totT=3.0d0
+C--------------------------------------------------------
+C print *,"wchodze"
+ dist=0.0d0
+ Eafmforce=0.0d0
+ do i=1,3
+ diffafm(i)=c(i,afmend)-c(i,afmbeg)
+ dist=dist+diffafm(i)**2
+ enddo
+ dist=dsqrt(dist)
+ Eafmforce=0.5d0*forceAFMconst
+ & *(distafminit+totTafm*velAFMconst-dist)**2
+C Eafmforce=-forceAFMconst*(dist-distafminit)
+ do i=1,3
+ gradafm(i,afmend-1)=-forceAFMconst*
+ &(distafminit+totTafm*velAFMconst-dist)
+ &*diffafm(i)/dist
+ gradafm(i,afmbeg-1)=forceAFMconst*
+ &(distafminit+totTafm*velAFMconst-dist)
+ &*diffafm(i)/dist
+ enddo
+C print *,'AFM',Eafmforce,totTafm*velAFMconst,dist
+ return
+ end
open(istat,file=statname,access="append")
#endif
#endif
+ if (AFMlog.gt.0) then
+ if (refstr) then
+ call rms_nac_nnc(rms,frac,frac_nn,co,.false.)
+ write (line1,'(i10,f15.2,3f12.3,f7.2,2f6.3,4f12.3,i5,$)')
+ & itime,totT,EK,potE,totE,
+ & rms,frac,frac_nn,kinetic_T,t_bath,gyrate(),
+ & potEcomp(23),me
+ format1="a133"
+ else
+C print *,'A CHUJ',potEcomp(23)
+ write (line1,'(i10,f15.2,7f12.3,i5,$)')
+ & itime,totT,EK,potE,totE,
+ & kinetic_T,t_bath,gyrate(),
+ & potEcomp(23),me
+ format1="a114"
+ endif
+ else if (selfguide.gt.0) then
+ distance=0.0
+ do j=1,3
+ distance=distance+(c(j,afmend)-c(j,afmbeg))**2
+ enddo
+ distance=dsqrt(distance)
+ if (refstr) then
+ call rms_nac_nnc(rms,frac,frac_nn,co,.false.)
+ write (line1,'(i10,f15.2,3f12.3,f7.2,2f6.3,f12.3,f10.1,2f8.2,
+ & f9.2,i5,$)')
+ & itime,totT,EK,potE,totE,
+ & rms,frac,frac_nn,kinetic_T,t_bath,gyrate(),
+ & distance,potEcomp(23),me
+ format1="a133"
+C print *,"CHUJOWO"
+ else
+C print *,'A CHUJ',potEcomp(23)
+ write (line1,'(i10,f15.2,8f12.3,i5,$)')
+ & itime,totT,EK,potE,totE,
+ & kinetic_T,t_bath,gyrate(),
+ & distance,potEcomp(23),me
+ format1="a114"
+ endif
+ else
if (refstr) then
call rms_nac_nnc(rms,frac,frac_nn,co,.false.)
write (line1,'(i10,f15.2,3f12.3,f7.2,4f6.3,3f12.3,i5,$)')
& amax,kinetic_T,t_bath,gyrate(),me
format1="a114"
endif
+ endif
if(usampl.and.totT.gt.eq_time) then
write(line2,'(i5,2f9.4,300f7.4)') iset,uconst,uconst_back,
& (qfrag(ii1),ii1=1,nfrag),(qpair(ii2),ii2=1,npair),
#ifdef DEBUG
write (iout,*) "gcart, gxcart, gloc before int_to_cart"
#endif
- do i=1,nct
+ do i=0,nct
do j=1,3
gcart(j,i)=gradc(j,i,icg)
gxcart(j,i)=gradx(j,i,icg)
C
C Initialize Cartesian-coordinate gradient
C
- do i=1,nres
+ do i=-1,nres
do j=1,3
gvdwx(j,i)=0.0D0
gradx_scp(j,i)=0.0D0
gradx(j,i,icg)=0.0d0
gscloc(j,i)=0.0d0
gsclocx(j,i)=0.0d0
+ gliptranc(j,i)=0.0d0
+ gliptranx(j,i)=0.0d0
+ gradafm(j,i)=0.0d0
do intertyp=1,3
gloc_sc(intertyp,i,icg)=0.0d0
enddo
icsa_in=40
crc for ifc error 118
icsa_pdb=42
+C Lipidic input file for parameters range 60-79
+ iliptranpar=60
+C input file for transfer sidechain and peptide group inside the
+C lipidic environment if lipid is implicite
+
+C DNA input files for parameters range 80-99
+C Suger input files for parameters range 100-119
+C All-atom input files for parameters range 120-149
C
C Set default weights of the energy terms.
C
enddo
do i=1,ntyp
do j=1,ntyp
- aa(i,j)=0.0D0
- bb(i,j)=0.0D0
+ aa_aq(i,j)=0.0D0
+ bb_aq(i,j)=0.0D0
+ aa_lip(i,j)=0.0D0
+ bb_lip(i,j)=0.0D0
augm(i,j)=0.0D0
sigma(i,j)=0.0D0
r0(i,j)=0.0D0
jhpb(i)=0
enddo
C Initialize correlation arrays
- do i=-maxtor,maxtor
+ do i=1,maxres
do k=1,2
b1(k,i)=0.0
b2(k,i)=0.0
b1tilde(k,i)=0.0
c b2tilde(k,i)=0.0
do j=1,2
+C CC(j,k,i)=0.0
+C Ctilde(j,k,i)=0.0
+C DD(j,k,i)=0.0
+C Dtilde(j,k,i)=0.0
+ EE(j,k,i)=0.0
+ enddo
+ enddo
+ enddo
+ do i=-maxtor,maxtor
+ do k=1,2
+ do j=1,2
CC(j,k,i)=0.0
Ctilde(j,k,i)=0.0
DD(j,k,i)=0.0
Dtilde(j,k,i)=0.0
- EE(j,k,i)=0.0
enddo
- enddo
+ enddo
enddo
C
C Initialize timing.
call int_bounds(nct-nnt,ibondp_start,ibondp_end)
ibondp_start=ibondp_start+nnt
ibondp_end=ibondp_end+nnt
+ call int_bounds(nres,ilip_start,ilip_end)
+ ilip_start=ilip_start
call int_bounds1(nres-1,ivec_start,ivec_end)
c print *,"Processor",myrank,fg_rank,fg_rank1,
c & " ivec_start",ivec_start," ivec_end",ivec_end
iset_end=nres+1
iint_start=2
iint_end=nres-1
+ ilip_start=1
+ ilip_end=nres
#endif
return
end
include 'COMMON.MD'
include 'COMMON.IOUNITS'
include 'COMMON.SCCOR'
-c calculating dE/ddc1
+ include 'COMMON.CONTROL'
+c calculating dE/ddc1
+C print *,"wchodze22",ialph(2,1)
if (nres.lt.3) go to 18
do j=1,3
gcart(j,1)=gcart(j,1)+gloc(1,icg)*dphi(j,1,4)
& gloc(ialph(2,1)+nside,icg)*domega(j,1,2)
endif
enddo
+C print *,"wchodze22",ialph(2,1)
c Calculating the remainder of dE/ddc2
do j=1,3
gcart(j,2)=gcart(j,2)+gloc(1,icg)*dphi(j,2,4)+
gcart(j,2)=gcart(j,2)+gloc(2,icg)*dphi(j,1,5)
endif
enddo
+C print *,"wchodze22",ialph(2,1)
c If there are only five residues
if(nres.eq.5) then
do j=1,3
endif
c If there are more than five residues
if(nres.gt.5) then
+C print *,"wchodze22",ialph(2,1)
do i=3,nres-3
+C print *,i,ialph(i,1)+nside
do j=1,3
gcart(j,i)=gcart(j,i)+gloc(i-2,icg)*dphi(j,3,i+1)
& +gloc(i-1,icg)*dphi(j,2,i+2)+
& gloc(i,icg)*dphi(j,1,i+3)+gloc(nres+i-4,icg)*dtheta(j,2,i+1)+
& gloc(nres+i-3,icg)*dtheta(j,1,i+2)
- if(itype(i).ne.10) then
+ if((itype(i).ne.10).and.(itype(i).ne.ntyp1)) then
gcart(j,i)=gcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,2,i)+
& gloc(ialph(i,1)+nside,icg)*domega(j,2,i)
endif
- if(itype(i+1).ne.10) then
+ if((itype(i+1).ne.10).and.(itype(i+1).ne.ntyp1)) then
gcart(j,i)=gcart(j,i)+gloc(ialph(i+1,1),icg)*dalpha(j,1,i+1)
& +gloc(ialph(i+1,1)+nside,icg)*domega(j,1,i+1)
endif
enddo
enddo
endif
+C print *,"wchodze22",ialph(2,1)
+
c Setting dE/ddnres-2
if(nres.gt.5) then
do j=1,3
c gloc(i,icg)=0.0D0
c write (iout,*) "poczotkoawy",i,gloc_sc(1,i,icg)
c enddo
+C print *,"tu dochodze??"
if (nres.lt.2) return
if ((nres.lt.3).and.(itype(1).eq.10)) return
if ((itype(1).ne.10).and.(itype(1).ne.ntyp1)) then
enddo
endif
c The side-chain vector derivatives
+C if (SELFGUIDE.gt.0) then
+C do j=1,3
+C gcart(j,afmbeg)=gcart(j,afmbeg)+gcart(j,afmend)
+C gcart(j,afmbeg)=0.0d0
+C gcart(j,afmend)=0.0d0
+C enddo
+C endif
return
end
enddo
enddo
endif
+C reading lipid parameters
+ read(iliptranpar,*) pepliptran
+ do i=1,ntyp
+ read(iliptranpar,*) liptranene(i)
+ enddo
+ close(iliptranpar)
#ifdef CRYST_THETA
C
C Read the parameters of the probability distribution/energy expression
EEold(2,1,-i)=-b(12,i)+b(13,i)
EEold(1,2,-i)=-b(12,i)-b(13,i)
write(iout,*) "TU DOCHODZE"
+ print *,"JESTEM"
c ee(1,1,i)=1.0d0
c ee(2,2,i)=1.0d0
c ee(2,1,i)=0.0d0
read (isidep,*,end=116,err=116)(sigii(i),i=1,ntyp)
read (isidep,*,end=116,err=116)(chip(i),i=1,ntyp)
read (isidep,*,end=116,err=116)(alp(i),i=1,ntyp)
+C now we start reading lipid
+ do i=1,ntyp
+ read (isidep,*,end=1161,err=1161)(epslip(i,j),j=i,ntyp)
+ print *,"WARNING!!"
+ do j=1,ntyp
+ epslip(i,j)=epslip(i,j)+0.05d0
+ enddo
+ enddo
C For the GB potential convert sigma'**2 into chi'
if (ipot.eq.4) then
do i=1,ntyp
do i=2,ntyp
do j=1,i-1
eps(i,j)=eps(j,i)
+ epslip(i,j)=epslip(j,i)
enddo
enddo
do i=1,ntyp
epsij=eps(i,j)
sigeps=dsign(1.0D0,epsij)
epsij=dabs(epsij)
- aa(i,j)=epsij*rrij*rrij
- bb(i,j)=-sigeps*epsij*rrij
- aa(j,i)=aa(i,j)
- bb(j,i)=bb(i,j)
+ aa_aq(i,j)=epsij*rrij*rrij
+ bb_aq(i,j)=-sigeps*epsij*rrij
+ aa_aq(j,i)=aa_aq(i,j)
+ bb_aq(j,i)=bb_aq(i,j)
+ epsijlip=epslip(i,j)
+ sigeps=dsign(1.0D0,epsijlip)
+ epsijlip=dabs(epsijlip)
+ aa_lip(i,j)=epsijlip*rrij*rrij
+ bb_lip(i,j)=-sigeps*epsijlip*rrij
+ aa_lip(j,i)=aa_lip(i,j)
+ bb_lip(j,i)=bb_lip(i,j)
if (ipot.gt.2) then
sigt1sq=sigma0(i)**2
sigt2sq=sigma0(j)**2
endif
if (lprint) then
write (iout,'(2(a3,2x),3(1pe10.3),5(0pf8.3))')
- & restyp(i),restyp(j),aa(i,j),bb(i,j),augm(i,j),
+ & restyp(i),restyp(j),aa_aq(i,j),bb_aq(i,j),augm(i,j),
& sigma(i,j),r0(i,j),chi(i,j),chi(j,i)
endif
enddo
goto 999
116 write (iout,*) "Error reading electrostatic energy parameters."
goto 999
+ 1161 write (iout,*) "Error reading electrostatic energy parameters.Lip"
+ goto 999
117 write (iout,*) "Error reading side chain interaction parameters."
goto 999
118 write (iout,*) "Error reading SCp interaction parameters."
endif
C Start new residue.
c write (iout,'(a80)') card
- read (card(24:26),*) ires
+ read (card(23:26),*) ires
read (card(18:20),'(a3)') res
if (ibeg.eq.1) then
ishift=ires-1
hfrag(i,j)=hfrag(i,j)-ishift
enddo
enddo
-
return
end
c---------------------------------------------------------------------------
refstr=pdbref .or. (index(controlcard,'REFSTR').gt.0)
indpdb=index(controlcard,'PDBSTART')
extconf=(index(controlcard,'EXTCONF').gt.0)
+ AFMlog=(index(controlcard,'AFM'))
+ selfguide=(index(controlcard,'SELFGUIDE'))
+ print *,'AFMlog',AFMlog,selfguide,"KUPA"
call readi(controlcard,'IPRINT',iprint,0)
call readi(controlcard,'MAXGEN',maxgen,10000)
call readi(controlcard,'MAXOVERLAP',maxoverlap,1000)
c Cutoff range for interactions
call reada(controlcard,"R_CUT",r_cut,15.0d0)
call reada(controlcard,"LAMBDA",rlamb,0.3d0)
+ call reada(controlcard,"LIPTHICK",lipthick,0.0d0)
+ call reada(controlcard,"LIPAQBUF",lipbufthick,0.0d0)
+ if (lipthick.gt.0.0d0) then
+ bordliptop=(boxzsize+lipthick)/2.0
+ bordlipbot=bordliptop-lipthick
+C endif
+ if ((bordliptop.gt.boxzsize).or.(borlipbot.lt.0.0))
+ & write(iout,*) "WARNING WRONG SIZE OF LIPIDIC PHASE"
+ buflipbot=bordlipbot+lipbufthick
+ bufliptop=bordliptop-lipbufthick
+ if ((lipbufthick*2.0d0).gt.lipthick)
+ &write(iout,*) "WARNING WRONG SIZE OF LIP AQ BUF"
+ endif
+ write(iout,*) "bordliptop=",bordliptop
+ write(iout,*) "bordlipbot=",bordlipbot
+ write(iout,*) "bufliptop=",bufliptop
+ write(iout,*) "buflipbot=",buflipbot
+
+
if (me.eq.king .or. .not.out1file )
& write (iout,*) "DISTCHAINMAX",distchainmax
call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
call reada(weightcard,'TEMP0',temp0,300.0d0)
+ call reada(weightcard,'WLT',wliptran,0.0D0)
if (index(weightcard,'SOFT').gt.0) ipot=6
C 12/1/95 Added weight for the multi-body term WCORR
call reada(weightcard,'WCORRH',wcorr,1.0D0)
call flush(iout)
if (constr_dist.gt.0) call read_dist_constr
write (iout,*) "After read_dist_constr nhpb",nhpb
+ if ((AFMlog.gt.0).or.(selfguide.gt.0)) call read_afminp
call hpb_partition
if(me.eq.king.or..not.out1file)
& write (iout,*) 'Contact order:',co
open (ielep,file=elename,status='old',readonly)
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old',readonly)
+ call getenv_loc('LIPTRANPAR',liptranname)
+ open (iliptranpar,file=liptranname,status='old',action='read')
#ifndef CRYST_SC
call getenv_loc('ROTPARPDB',rotname_pdb)
open (irotam_pdb,file=rotname_pdb,status='old',action='read')
include 'COMMON.MD'
open(irest2,file=rest2name,status='unknown')
read(irest2,*) totT,EK,potE,totE,t_bath
+ totTafm=totT
do i=1,2*nres
read(irest2,'(3e15.5)') (d_t(j,i),j=1,3)
enddo
enddo
return
end
+C---------------------------------------------------------------------------
+ subroutine read_afminp
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+ include 'COMMON.SETUP'
+ include 'COMMON.CONTROL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.SBRIDGE'
+ character*320 afmcard
+ print *, "wchodze"
+ call card_concat(afmcard)
+ call readi(afmcard,"BEG",afmbeg,0)
+ call readi(afmcard,"END",afmend,0)
+ call reada(afmcard,"FORCE",forceAFMconst,0.0d0)
+ call reada(afmcard,"VEL",velAFMconst,0.0d0)
+ print *,'FORCE=' ,forceAFMconst
+CCCC NOW PROPERTIES FOR AFM
+ distafminit=0.0d0
+ do i=1,3
+ distafminit=(c(i,afmend)-c(i,afmbeg))**2+distafminit
+ enddo
+ distafminit=dsqrt(distafminit)
+ print *,'initdist',distafminit
+ return
+ end
+
c-------------------------------------------------------------------------------
subroutine read_dist_constr
implicit real*8 (a-h,o-z)
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
+ xi=mod(xi,boxxsize)
+ if (xi.lt.0) xi=xi+boxxsize
+ yi=mod(yi,boxysize)
+ if (yi.lt.0) yi=yi+boxysize
+ zi=mod(zi,boxzsize)
+ if (zi.lt.0) zi=zi+boxzsize
+ if ((zi.gt.bordlipbot)
+ &.and.(zi.lt.bordliptop)) then
+C the energy transfer exist
+ if (zi.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((positi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick)
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipi=1.0d0
+ ssgradlipi=0.0
+ endif
+ else
+ sslipi=0.0d0
+ ssgradlipi=0.0
+ endif
+
dxi=dc_norm(1,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
c alf1=0.0D0
c alf2=0.0D0
c alf12=0.0D0
- xj=c(1,nres+j)-xi
- yj=c(2,nres+j)-yi
- zj=c(3,nres+j)-zi
+C xj=c(1,nres+j)-xi
+C yj=c(2,nres+j)-yi
+C zj=c(3,nres+j)-zi
+ xj=c(1,nres+j)
+ yj=c(2,nres+j)
+ zj=c(3,nres+j)
+ xj=mod(xj,boxxsize)
+ if (xj.lt.0) xj=xj+boxxsize
+ yj=mod(yj,boxysize)
+ if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+ if ((zj.gt.bordlipbot)
+ &.and.(zj.lt.bordliptop)) then
+C the energy transfer exist
+ if (zj.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((positi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick)
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipj=1.0d0
+ ssgradlipj=0.0
+ endif
+ else
+ sslipj=0.0d0
+ ssgradlipj=0.0
+ endif
+ aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +aa_aq(itypi,itypj)*(2.0d0-sslipi+sslipj)/2.0d0
+ bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +bb_aq(itypi,itypj)*(2.0d0-sslipi+sslipj)/2.0d0
+
+ dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ xj_safe=xj
+ yj_safe=yj
+ zj_safe=zj
+ subchap=0
+ do xshift=-1,1
+ do yshift=-1,1
+ do zshift=-1,1
+ xj=xj_safe+xshift*boxxsize
+ yj=yj_safe+yshift*boxysize
+ zj=zj_safe+zshift*boxzsize
+ dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ if(dist_temp.lt.dist_init) then
+ dist_init=dist_temp
+ xj_temp=xj
+ yj_temp=yj
+ zj_temp=zj
+ subchap=1
+ endif
+ enddo
+ enddo
+ enddo
+ if (subchap.eq.1) then
+ xj=xj_temp-xi
+ yj=yj_temp-yi
+ zj=zj_temp-zi
+ else
+ xj=xj_safe-xi
+ yj=yj_safe-yi
+ zj=zj_safe-zi
+ endif
+
dxj=dc_norm(1,nres+j)
dyj=dc_norm(2,nres+j)
dzj=dc_norm(3,nres+j)
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
rij=dsqrt(rrij)
+ sss=sscale((1.0d0/rij)/sigma(itypi,itypj))
+ sssgrad=sscagrad((1.0d0/rij)/sigma(itypi,itypj))
+
C Calculate angle-dependent terms of energy and contributions to their
C derivatives.
call sc_angular
c---------------------------------------------------------------
rij_shift=1.0D0/rij_shift
fac=rij_shift**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+evdwij
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa
cd write (iout,'(2(a3,i3,2x),17(0pf7.3))')
cd & restyp(itypi),i,restyp(itypj),j,
cd & epsi,sigm,chi1,chi2,chip1,chip2,
fac=-expon*(e1+evdwij)*rij_shift
sigder=fac*sigder
fac=rij*fac
+ fac=fac+evdwij/sss*sssgrad/sigma(itypi,itypj)*rij
C Calculate the radial part of the gradient
gg(1)=xj*fac
gg(2)=yj*fac
gg(3)=zj*fac
+ gg_lipi(3)=ssgradlipi*evdwij
+ gg_lipj(3)=ssgradlipj*evdwij
C Calculate angular part of the gradient.
call sc_grad
ENDIF
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
dsci_inv=vbld_inv(i+nres)
-
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+ xi=mod(xi,boxxsize)
+ if (xi.lt.0) xi=xi+boxxsize
+ yi=mod(yi,boxysize)
+ if (yi.lt.0) yi=yi+boxysize
+ zi=mod(zi,boxzsize)
+ if (zi.lt.0) zi=zi+boxzsize
+C define scaling factor for lipids
+
+C if (positi.le.0) positi=positi+boxzsize
+C print *,i
+C first for peptide groups
+c for each residue check if it is in lipid or lipid water border area
+ if ((zi.gt.bordlipbot)
+ &.and.(zi.lt.bordliptop)) then
+C the energy transfer exist
+ if (zi.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((positi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick)
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipi=1.0d0
+ ssgradlipi=0.0
+ endif
+ else
+ sslipi=0.0d0
+ ssgradlipi=0.0
+ endif
itypj=itype(j)
- xj=c(1,nres+j)-c(1,nres+i)
- yj=c(2,nres+j)-c(2,nres+i)
- zj=c(3,nres+j)-c(3,nres+i)
+ xj=c(1,nres+j)
+ yj=c(2,nres+j)
+ zj=c(3,nres+j)
+ xj=mod(xj,boxxsize)
+ if (xj.lt.0) xj=xj+boxxsize
+ yj=mod(yj,boxysize)
+ if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+ if ((zj.gt.bordlipbot)
+ &.and.(zj.lt.bordliptop)) then
+C the energy transfer exist
+ if (zj.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((positi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick)
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipj=1.0d0
+ ssgradlipj=0.0
+ endif
+ else
+ sslipj=0.0d0
+ ssgradlipj=0.0
+ endif
+ aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +aa_aq(itypi,itypj)*(2.0d0-sslipi+sslipj)/2.0d0
+ bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +bb_aq(itypi,itypj)*(2.0d0-sslipi+sslipj)/2.0d0
+
+ dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ xj_safe=xj
+ yj_safe=yj
+ zj_safe=zj
+ subchap=0
+ xj_safe=xj
+ yj_safe=yj
+ zj_safe=zj
+ subchap=0
+ do xshift=-1,1
+ do yshift=-1,1
+ do zshift=-1,1
+ xj=xj_safe+xshift*boxxsize
+ yj=yj_safe+yshift*boxysize
+ zj=zj_safe+zshift*boxzsize
+ dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ if(dist_temp.lt.dist_init) then
+ dist_init=dist_temp
+ xj_temp=xj
+ yj_temp=yj
+ zj_temp=zj
+ subchap=1
+ endif
+ enddo
+ enddo
+ enddo
+ if (subchap.eq.1) then
+ xj=xj_temp-xi
+ yj=yj_temp-yi
+ zj=zj_temp-zi
+ else
+ xj=xj_safe-xi
+ yj=yj_safe-yi
+ zj=zj_safe-zi
+ endif
+
+C xj=c(1,nres+j)-c(1,nres+i)
+C yj=c(2,nres+j)-c(2,nres+i)
+C zj=c(3,nres+j)-c(3,nres+i)
dxj=dc_norm(1,nres+j)
dyj=dc_norm(2,nres+j)
dzj=dc_norm(3,nres+j)
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
rij=dsqrt(rrij) ! sc_angular needs rij to really be the inverse
+ sss=sscale((1.0d0/rij)/sigma(itypi,itypj))
+ sssgrad=sscagrad((1.0d0/rij)/sigma(itypi,itypj))
c The following are set in sc_angular
c erij(1)=xj*rij
c erij(2)=yj*rij
ljXs=sig-sig0ij
ljA=eps1*eps2rt**2*eps3rt**2
- ljB=ljA*bb(itypi,itypj)
- ljA=ljA*aa(itypi,itypj)
- ljxm=ljXs+(-2.0D0*aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
+ ljB=ljA*bb
+ ljA=ljA*aa
+ ljxm=ljXs+(-2.0D0*aa/bb)**(1.0D0/6.0D0)
ssXs=d0cm
deltat1=1.0d0-om1
c Stop and plot energy and derivative as a function of distance
if (checkstop) then
ssm=ssC-0.25D0*ssB*ssB/ssA
- ljm=-0.25D0*ljB*bb(itypi,itypj)/aa(itypi,itypj)
+ ljm=-0.25D0*ljB*bb/aa
if (ssm.lt.ljm .and.
& dabs(rij-0.5d0*(ssxm+ljxm)).lt.0.35d0*(ljxm-ssxm)) then
nicheck=1000
havebond=.false.
ljd=rij-ljXs
fac=(1.0D0/ljd)**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa
+ e2=fac*bb
eij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=eij*eps3rt
eps3der=eij*eps2rt
- eij=eij*eps2rt*eps3rt
+ eij=eij*eps2rt*eps3rt*sss
sigder=-sig/sigsq
e1=e1*eps1*eps2rt**2*eps3rt**2
ed=-expon*(e1+eij)/ljd
sigder=ed*sigder
+ ed=ed+eij/sss*sssgrad/sigma(itypi,itypj)*rij
eom1=eps2der*eps2rt_om1-2.0D0*alf1*eps3der+sigder*sigsq_om1
eom2=eps2der*eps2rt_om2+2.0D0*alf2*eps3der+sigder*sigsq_om2
eom12=eij*eps1_om12+eps2der*eps2rt_om12
havebond=.true.
ssd=rij-ssXs
eij=ssA*ssd*ssd+ssB*ssd+ssC
-
+ eij=eij*sss
ed=2*akcm*ssd+akct*deltat12
+ ed=ed+eij/sss*sssgrad/sigma(itypi,itypj)*rij
pom1=akct*ssd
pom2=v1ss+2*v2ss*cosphi+3*v3ss*cosphi*cosphi
eom1=-2*akth*deltat1-pom1-om2*pom2
fac1=deltasq_inv*fac*(xm-rij)
fac2=deltasq_inv*fac*(rij-ssxm)
ed=delta_inv*(Ht*hd2-ssm*hd1)
+ eij=eij*sss
+ ed=ed+eij/sss*sssgrad/sigma(itypi,itypj)*rij
eom1=fac1*d_ssxm(1)+fac2*d_xm(1)+h1*d_ssm(1)
eom2=fac1*d_ssxm(2)+fac2*d_xm(2)+h1*d_ssm(2)
eom12=fac1*d_ssxm(3)+fac2*d_xm(3)+h1*d_ssm(3)
else
havebond=.false.
- ljm=-0.25D0*ljB*bb(itypi,itypj)/aa(itypi,itypj)
- d_ljm(1)=-0.5D0*bb(itypi,itypj)/aa(itypi,itypj)*ljB
+ ljm=-0.25D0*ljB*bb/aa
+ d_ljm(1)=-0.5D0*bb/aa*ljB
d_ljm(2)=d_ljm(1)*(0.5D0*eps2rt_om2/eps2rt+alf2/eps3rt)
d_ljm(3)=d_ljm(1)*(0.5D0*eps1_om12+0.5D0*eps2rt_om12/eps2rt-
+ alf12/eps3rt)
fac1=deltasq_inv*fac*(ljxm-rij)
fac2=deltasq_inv*fac*(rij-xm)
ed=delta_inv*(ljm*hd2-Ht*hd1)
+ eij=eij*sss
+ ed=ed+eij/sss*sssgrad/sigma(itypi,itypj)*rij
eom1=fac1*d_xm(1)+fac2*d_ljxm(1)+h2*d_ljm(1)
eom2=fac1*d_xm(2)+fac2*d_ljxm(2)+h2*d_ljm(2)
eom12=fac1*d_xm(3)+fac2*d_ljxm(3)+h2*d_ljm(3)
checkstop=.false.
endif
c-------END TESTING CODE
+ gg_lipi(3)=ssgradlipi*eij
+ gg_lipj(3)=ssgradlipj*eij
do k=1,3
dcosom1(k)=(dc_norm(k,nres+i)-om1*erij(k))/rij
gg(k)=ed*erij(k)+eom1*dcosom1(k)+eom2*dcosom2(k)
enddo
do k=1,3
- gvdwx(k,i)=gvdwx(k,i)-gg(k)
+ gvdwx(k,i)=gvdwx(k,i)-gg(k)+gg_lipi(k)
& +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))
& +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
- gvdwx(k,j)=gvdwx(k,j)+gg(k)
+ gvdwx(k,j)=gvdwx(k,j)+gg(k)+gg_lipj(k)
& +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j))
& +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
enddo
cgrad enddo
do l=1,3
- gvdwc(l,i)=gvdwc(l,i)-gg(l)
- gvdwc(l,j)=gvdwc(l,j)+gg(l)
+ gvdwc(l,i)=gvdwc(l,i)-gg(l)+gg_lipi(k)
+ gvdwc(l,j)=gvdwc(l,j)+gg(l)+gg_lipj(k)
enddo
return
projects / unres.git / commitdiff