changes in shielding

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
new file mode 100644 (file)
index 0000000..3adbfc8
--- /dev/null
+++ b/PARAM/sc_GB_opt_ext.1gab_3S_qclass5no310-shan2-sc-16-10-8k_lip
@@ -0,0 +1,244 @@
+    4    6
+   5.605353726100000   6.220003215400000   6.215989849600000   6.438696896300000
+   6.209810123100000   5.959637479800000   5.431022266200000   4.879008525700000
+   5.263842382200000   5.496195412400000   4.292812416200000   4.358225054000000
+   4.266775592100000   3.681384595800000   3.540542964700000   3.702698591200000
+   4.717759615600000   3.381199222700000   3.793608545800000   4.515749058500000
+   6.220003215400000   6.215989849600000   5.496195412400000   5.496195412400000
+
+   6.629674668000000   6.671726050800000   6.816887694500000   6.837896015200000
+   6.351203998600000   6.142519242300000   5.520020640600000   5.485893602400000
+   4.938257326200000   4.279512916600000   4.053485701800000   4.208642852500000
+   3.538808627900000   3.420973032700000   2.799574419300000   4.816426855300000
+   3.879075507100000   3.587826217700000   4.645743255500000   6.629674668000000
+   6.671726050800000   5.485893602400000   5.485893602400000
+
+   5.434261193691611   6.009504353949445   5.751833613689151   4.388369927131041
+   6.139482146000000   4.432779364180328   3.635448013213493   3.042556269070575
+   1.858255457238648   3.619846653665197   3.902273188000000   2.840826371233924 
+   1.901219059651194   3.010635482615414   2.681361243261458   3.871192813400000
+   3.639660062795308   4.487266103000000   6.671726050800000   5.434261193691611
+   3.635448013213493   3.635448013213493
+
+   7.144249845164532   5.950132764851209   5.636408114630104   6.256568766200000
+   4.721753486138623   5.072743940945156   4.725634408062251   3.773513014441411
+   3.537762800513723   4.309235277900000   4.002278495651890   4.124103654261368
+   1.771213000543424   3.864752062532702   4.468184401000000   4.481956278333824
+   4.902394508200000   6.816887694500000   6.009504353949445   5.072743940945156
+   5.072743940945156
+
+   5.956274037802311   7.211686591187319   6.204787608200000   5.376059458542183
+   5.023511032618925   3.156887023825594   2.932344993803476   2.999897908513799
+   3.895407345300000   2.991138620007669   2.096199593475473   1.780803572610500
+   3.558049006448599   4.023841260600000   3.682633555857166   4.808718037700000
+   6.837896015200000   5.751833613689151   5.023511032618925   5.023511032618925
+
+   5.741243604492526   5.884448203300000   3.398137040446693   5.432746439707773
+   4.729707784043235   3.970010356404483   3.414577863946629   3.650628980600000
+   2.605234605568324   2.392978757746573   3.096075853472831   4.009206356643173
+   3.441595274000000   3.721594130855455   4.593424600900000   6.351203998600000
+   4.388369927131041   5.432746439707773   5.432746439707773
+
+   5.282881132500000   4.829846631500000   4.757532777700000   4.724977904200000
+   3.565638428500000   3.561336656700000   3.927304556400000   3.766477911800000
+   3.586169976100000   3.552319162700000   4.650867246300000   4.242430826000000
+   4.098772778300000   4.507966992900000   6.142519242300000   6.139482146000000
+   4.757532777700000   4.757532777700000   
+ 
+   4.222264575400000   3.568880377430671   1.710507474941357   0.726915001472055
+   2.519422404183540   3.136598518800000   2.564808696931206   3.101026335222954
+   2.213396947938416   3.343125814753411   3.444306825200000   2.416478592751639
+   4.091530576300000   5.520020640600000   4.432779364180328   1.710507474941357
+   1.710507474941357
+
+   4.157487725645439   3.262380685905436   2.953659747759453   1.237209789211462
+   2.500185737000000   1.984183152198450   1.368828812773212   2.060401072298498
+   2.863410468895249   2.015232903800000   1.541966676954322   3.639585254600000
+   5.485893602400000   3.635448013213493   3.262380685905436   3.262380685905436
+
+   2.501655793500000   2.394681323067151   2.071384505085577   1.074154474700000
+   0.985099710786774   0.001985439127056   0.921773098679111   5.126752085199419
+   1.500212764900000  -0.018286801754111   3.538112898500000   4.938257326200000
+   3.042556269070575   2.501655793500000   2.501655793500000
+
+   2.248058879145623   2.683627337507786   1.505360785600000  -0.706299059260768
+   1.284606704482992   1.109202790492530   2.070407759035996   1.983305353800000
+  -0.008577364700000   2.955755366600000   4.279512916600000   1.858255457238648
+   2.394681323067151   2.394681323067151
+
+   1.280003824300000   0.768980610000000   0.625889188870640   1.535343520692143
+   0.574105444778441   1.174671233709513   1.497548217400000  -0.665902088339257
+   2.941502147900000   4.053485701800000   3.619846653665197   2.071384505085577
+   2.071384505085577
+
+  -0.679242885900000   0.453238323900000  -0.759038766000000  -0.361703484600000
+   1.680327505800000   0.677520998800000  -0.535483746800000   2.620859136300000
+   4.208642852500000   3.902273188000000   1.074154474700000   1.074154474700000
+
+   0.290068410287431  -0.092399325129687   1.982203632452388   0.078357579868221
+   0.389638827500000  -0.177470106993247   2.325532607700000   3.538808627900000
+   2.840826371233924   0.985099710786774   0.985099710786774
+
+  -3.392465857895507  -1.871634582322480   1.071505323254014   2.748917412400000
+   1.802089391960750   1.797571866700000   3.420973032700000   1.90121905965119
+   0.001985439127056   0.001985439127056   
+
+  -1.397996047062832   0.263585152937208   2.820287379000000   1.642062410367716
+   1.862509124700000   2.799574419300000   3.010635482615414   0.921773098679111
+   0.921773098679111
+
+   3.729277869700000   2.294443648100000  -0.070327972331951   3.111577617700000
+   4.816426855300000   2.681361243261458   5.126752085199419   5.126752085199419
+
+  -0.082736296100000  -1.604311318200000   2.443983743500000   3.879075507100000
+   3.871192813400000   1.500212764900000   1.500212764900000
+
+  -3.048709356063184   2.366463453300000   3.587826217700000   3.639660062795308
+  -0.018286801754111  -0.018286801754111
+
+   4.192796926000000   4.645743255500000   4.487266103000000   3.538112898500000
+   3.538112898500000
+
+   6.629674668000000   6.671726050800000   5.485893602400000   5.485893602400000
+ 
+   5.434261193691611   3.635448013213493   3.635448013213493
+
+   2.501655793500000   2.501655793500000
+
+   2.501655793500000
+
+   2.674806001700000   2.733881014500000   2.966464722900000   2.881963673700000
+   3.021073815000000   2.841428615200000   2.477343866000000   2.461194378800000
+   2.465320121300000   2.492508737100000   2.573476775100000   2.456402674400000
+   2.484782528100000   2.488928923300000   2.508951764500000   2.508333838300000
+   2.422062272300000   2.271460977000000   2.452070308900000   2.702612978800000
+   2.733881014500000   3.239567000000000   2.465320121300000   2.465320121300000
+
+   4.927215476100000   5.105428423000000   4.207351616500000   4.851397283700000
+   2.784887529300000   3.582986163400000   7.866021757600000   7.429920984700000
+   1.962593983200000   0.798776956900000   4.058089968100000   1.888902103200000
+   3.198719702600000   3.267327453800000   2.684813190400000   2.004302740400000
+   6.244634191000000   8.195945209500000  13.474829585800000   2.663237683700000
+   7.005428423000000   4.207351616500000   1.962593983200000   1.888902103200000
+
+   0.869902301100000   1.054066001400000   0.938590929800000   1.026327410100000
+   1.083527704500000   1.054318388600000   0.788868699600000   0.898930583300000
+   1.003996287500000   1.242751812800000   0.893280172400000   0.917392899000000
+   1.615769565700000   1.431586037300000   2.049831787900000   1.419961554600000
+   0.993367797100000   1.431962560000000  27.495176328800000   0.778802528600000
+   1.446666701400000   0.868195759800000   1.000000000000300   0.917392899000000
+
+   0.010369755600000   0.061138567400000   0.044830334600000   0.039283178200000
+   0.085416633800000   0.039889661900000   0.024949656900000   0.023241090800000
+   0.086137910000000  -0.075479418500000  -0.026614602100000  -0.016342909900000  
+   0.057216710300000  -0.046860882500000   0.015104845500000   0.008496367800000
+   0.027893039700000   0.007692291100000   0.103353673800000  -0.009825603600000
+   0.061138567400000   0.044830334600000   0.086137910000000  -0.016342909900000
+  2.252000       2.758289       2.828747       2.573807
+   2.573807       2.314337       3.329045       3.123838
+   1.679138       1.245463       2.417517       2.138542
+   2.902927       2.675567       2.916240       2.690005
+   2.934561       3.360153       2.904943       2.252400
+   2.822849       3.512073       2.021838       2.021838
+
+   3.378400       3.464698       3.152444       3.152444
+   2.834641       4.077473       3.826132       2.056637
+   1.525464       2.961017       2.619323       3.555555
+   3.277081       3.571861       3.294765       3.594301
+   4.115573       3.558025       2.758779       3.457474
+   4.301648       2.476383       2.476383
+
+   3.553200       3.232970       3.232970       2.907049
+   4.181627       3.923866       2.109172       1.564431
+   3.036654       2.686231       3.646378       3.360790
+   3.663100       3.378926       3.686114       4.220702
+   3.648911       2.829249       3.545792       4.411529
+   2.539639       2.539639
+
+   2.941600       2.941600       2.645052       3.804760
+   3.570230       1.919084       1.423437       2.762977
+   2.444136       3.317750       3.057901       3.332965
+   3.074402       3.353905       3.840313       3.320055
+   2.574264       3.226230       4.013942       2.310756
+   2.310756
+
+   2.941600       2.645052       3.804760       3.570230
+   1.919084       1.423437       2.762977       2.444136
+   3.317750       3.057901       3.332965       3.074402
+   3.353905       3.840313       3.320055       2.574264
+   3.226230       4.013942       2.310756       2.310756
+
+   2.378400       3.421196       3.210309       1.725618
+   1.279938       2.484436       2.197739       2.983282
+   2.749629       2.996964       2.764467       3.015792
+   3.453165       2.985354       2.314748       2.900988
+   3.609290       2.077805       2.077805
+
+   4.921200       4.617850       2.482205       1.841120
+   3.573723       3.161325       4.291286       3.955188
+   4.310965       3.976531       4.338049       4.967185
+   4.294266       3.329637       4.172909       5.191762
+   2.988806       2.988806
+
+   4.333200       2.329199       1.727631       3.353434
+   2.966456       4.026765       3.711385       4.045231
+   3.731412       4.070646       4.661001       4.029562
+   3.124393       3.915686       4.871735       2.804572
+   2.804572
+
+   1.252000      0.9286429       1.802551       1.594541
+   2.164482       1.994958       2.174409       2.005723
+   2.188069       2.505400       2.165986       1.679436
+   2.104775       2.618674       1.507524       1.507524
+
+  0.6888000       1.337002       1.182715       1.605456
+   1.479715       1.612819       1.487700       1.622951
+   1.858324       1.606571       1.245684       1.561169
+   1.942343       1.118173       1.118173
+
+   2.595200       2.295720       3.116286       2.872216
+   3.130577       2.887715       3.150245       3.607117
+   3.118450       2.417947       3.030323       3.770203
+   2.170439       2.170439
+
+   2.030800       2.756675       2.540769       2.769316
+   2.554480       2.786715       3.190865       2.758589
+   2.138922       2.680631       3.335131       1.919976
+   1.919976
+
+   3.742000       3.448923       3.759161       3.467535
+   3.782778       4.331384       3.744599       2.903442
+   3.638776       4.527216       2.606238       2.606238
+
+   3.178800       3.464740       3.195954       3.486507
+   3.992146       3.451319       2.676042       3.353784
+   4.172640       2.402115       2.402115
+
+  -61.60000      -35.26000       3.800125       48.12500
+   35.00000       2.916757       3.655463       4.547977
+   2.618191       2.618191
+
+  -23.62500       3.505321       39.90000       28.44000
+   2.690483       3.371882       4.195157       2.415078
+   2.415078
+
+   3.824000       4.378585       3.785405       2.935082
+   3.678429       4.576550       2.634640       2.634640
+
+  -1.447000      -28.07000       3.360749       4.211903
+   5.240276       3.016734       3.016734
+
+  -76.82000       2.905459       3.641304       4.530360
+   2.608049       2.608049
+
+   2.252800       2.823350       3.512697       2.022197
+   2.022197
+
+   3.538400       4.402332       2.534345       2.534345
+
+   5.477200       3.153127       3.153127
+
+   1.815200       1.815200
+
+   1.815200
+

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 393ff9a..f524af3 100644 (file)
--- a/source/unres/src_MD-M/energy_p_new_barrier.F
+++ b/source/unres/src_MD-M/energy_p_new_barrier.F
@@ -1006,6 +1006,7 @@ c-------------------------------------------------------------------------------
       include 'COMMON.IOUNITS'
       include 'COMMON.FFIELD'
       include 'COMMON.SBRIDGE'
+      include 'COMMON.CONTROL'
       double precision kfac /2.4d0/
       double precision x,x2,x3,x4,x5,licznik /1.12692801104297249644/
 c      facT=temp0/t_bath
@@ -1041,6 +1042,11 @@ c      facT=2*temp0/(t_bath+temp0)
 #endif
        stop 555
       endif
+      if (shield_mode.gt.0) then
+       wscp=weights(2)*fact
+       wsc=weights(1)*fact
+       wvdwpp=weights(16)*fact
+      endif
       welec=weights(3)*fact
       wcorr=weights(4)*fact3
       wcorr5=weights(5)*fact4
@@ -11587,7 +11593,7 @@ C       cosphi_grad_loc(j)=0.0d0
 C      print *,sinphi,sinthet
       VofOverlap=VSolvSphere/2.0d0*(1.0d0-dsqrt(1.0d0-sinphi*sinthet))
      &                    /VSolvSphere_div
-     &                    *wshield
+C     &                    *wshield
 C now the gradient...
       do j=1,3
       grad_shield(j,i)=grad_shield(j,i)
@@ -11598,7 +11604,7 @@ C  gradient po costhet
      &(1.0d0/(-dsqrt(1.0d0-sinphi*sinthet))*(
      &       sinphi/sinthet*costhet*costhet_grad(j)
      &      +sinthet/sinphi*cosphi*cosphi_grad_long(j)))
-     & )*div77_81
+     & )*wshield
 C grad_shield_side is Cbeta sidechain gradient
       grad_shield_side(j,ishield_list(i),i)=
      &        (sh_frac_dist_grad(j)*-2.0d0
@@ -11607,18 +11613,18 @@ C grad_shield_side is Cbeta sidechain gradient
      &(1.0d0/(-dsqrt(1.0d0-sinphi*sinthet))*(
      &       sinphi/sinthet*costhet*costhet_grad(j)
      &      +sinthet/sinphi*cosphi*cosphi_grad_long(j)))
-     &       )*div77_81        
+     &       )*wshield        
 
        grad_shield_loc(j,ishield_list(i),i)=
      &       scale_fac_dist*VSolvSphere/VSolvSphere_div/2.0d0*
      &(1.0d0/(dsqrt(1.0d0-sinphi*sinthet))*(
      &       sinthet/sinphi*cosphi*cosphi_grad_loc(j)
      &        ))
-     &        *div77_81
+     &        *wshield
       enddo
       VolumeTotal=VolumeTotal+VofOverlap*scale_fac_dist
       enddo
-      fac_shield(i)=VolumeTotal*div77_81+div4_81
+      fac_shield(i)=VolumeTotal*wshield+(1.0d0-wshield)
 C      write(2,*) "TOTAL VOLUME",i,VolumeTotal,fac_shield(i)
       enddo
       return

diff --git a/source/unres/src_MD-M/readrtns_CSA.F b/source/unres/src_MD-M/readrtns_CSA.F
index 68fb297..9f72992 100644 (file)
--- a/source/unres/src_MD-M/readrtns_CSA.F
+++ b/source/unres/src_MD-M/readrtns_CSA.F
@@ -104,7 +104,7 @@ C constrains on theta angles WITH_THETA_CONSTR is the keyword
       with_theta_constr = index(controlcard,"WITH_THETA_CONSTR").gt.0
       write (iout,*) "with_theta_constr ",with_theta_constr
       call readi(controlcard,'SYM',symetr,1)
-      call reada(controlcard,'TIMLIM',timlim,960.0D0) ! default 16 hours
+      call reada(controlcard,'TIMLIM',timlim,2800.0D0) ! default 16 hours
       unres_pdb = index(controlcard,'UNRES_PDB') .gt. 0
       call reada(controlcard,'SAFETY',safety,30.0D0) ! default 30 minutes
       call reada(controlcard,'RMSDBC',rmsdbc,3.0D0)
@@ -782,7 +782,7 @@ C 12/1/95 Added weight for the multi-body term WCORR
           ss_depth=0.0
         endif
       endif
-
+      write (iout,*) "wshield,", wshield
       if(me.eq.king.or..not.out1file) then
        write (iout,*) "Parameters of the SS-bond potential:"
        write (iout,*) "D0CM",d0cm," AKCM",akcm," AKTH",akth,
@@ -1040,7 +1040,7 @@ c----------------------
           call MPI_Finalize(MPI_COMM_WORLD,IERROR)
           stop 'Error reading reference structure'
 #endif
-   39     call chainbuild
+   39     call chainbuild_extconf
           call setup_var
 czscore          call geom_to_var(nvar,coord_exp_zs(1,1))
           nstart_sup=nnt
@@ -1113,6 +1113,7 @@ C initial geometry.
             return
           else
             call read_angles(inp,*36)
+            call chainbuild_extconf
           endif
           goto 37
    36     write (iout,'(a)') 'Error reading angle file.'