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nanophere working
authorAdam Sieradzan <adasko@piasek4.chem.univ.gda.pl>
Thu, 26 Jan 2017 12:43:48 +0000 (13:43 +0100)
committerAdam Sieradzan <adasko@piasek4.chem.univ.gda.pl>
Thu, 26 Jan 2017 12:43:48 +0000 (13:43 +0100)
PARAM/TiO2.parm patch | blob | history
PARAM/TiO2_fin.parm [new file with mode: 0644] patch | blob
source/unres/src_MD-M/energy_p_new_barrier.F patch | blob | history
source/unres/src_MD-M/parmread.F patch | blob | history

diff --git a/PARAM/TiO2.parm b/PARAM/TiO2.parm
index e236309..cb975e5 100644 (file)
--- a/PARAM/TiO2.parm
+++ b/PARAM/TiO2.parm
@@ -1 +1,25 @@
-   1   0.286   4.508     1.491    -0.238    -2.215   3.922E-14 ! Cys\r   2   4.173   4.136  -143.035    28.494   180.705   1.086E-10 ! Met\r   1  10.793   4.152  -250.420    48.235   328.091   7.237E-11 ! Phe\r   2   9.872   3.799  -308.062    62.468   382.714   3.262E-10 ! Ile\r   2  12.025   4.056  -448.084    90.596   559.212   2.482E-10 ! Leu\r   1   3.929   3.894  -241.329    50.844   288.017   6.165E-10 ! Val\r   2   0.285   5.797   738.577  -155.331  -884.672   3.662E-09 ! Trp\r   1  29.509   4.046  -648.094   126.324   840.706   1.297E-10 ! Tyr\r   1   0.058   4.710     0.612    -0.108    -0.790  -3.640E-14 ! Ala\r   0   0.000   0.000     0.000     0.000     0.000   0.000E+00 ! Gly\r   1 163.545   1.976 -5996.349  1676.896  5422.473   5.557E-13 ! Thr\r   1 158.959   1.810 -8243.740  2491.600  6900.467   1.632E-11 ! Ser\r   3   1.582   3.601   673.244  -173.206  -646.238   4.709E-08 ! Gln\r   1   7.354   3.256  -485.919   112.979   530.772   9.510E-16 ! Asn\r   3  25.379   2.776  -729.290   168.012   800.982   2.274E-16 ! Glu\r   1  25.969   2.505  -711.633   167.698   761.605   8.831E-16 ! Asp\r   1   6.267   3.952  -176.750    35.322   222.723   1.641E-10 ! His\r   3   0.755   4.649     6.176    -0.945    -9.823   1.249E-13 ! Arg\r   3   0.001   8.312     2.122     0.132    -6.640   3.808E-11 ! Lys\r   1   0.000   0.000     0.000     0.000     0.000   0.000E+00 ! Pro\r
\ No newline at end of file
+   0.058   4.710                                            0.00 ! Pep                                        
+   0.286   4.508     1.491    -0.238    -2.215   3.922E-14  0.00 ! Cys
+   4.173   4.136  -143.035    28.494   180.705   1.086E-10  0.00 ! Met
+  10.793   4.152  -250.420    48.235   328.091   7.237E-11  0.00 ! Phe
+   9.872   3.799  -308.062    62.468   382.714   3.262E-10  0.00 ! Ile
+  12.025   4.056  -448.084    90.596   559.212   2.482E-10  0.00 ! Leu
+   3.929   3.894  -241.329    50.844   288.017   6.165E-10  0.00 ! Val
+   0.285   5.797   738.577  -155.331  -884.672   3.662E-09  0.00 ! Trp
+  29.509   4.046  -648.094   126.324   840.706   1.297E-10  0.00 ! Tyr
+   0.058   4.710     0.612    -0.108    -0.790  -3.640E-14  0.00 ! Ala
+   0.000   0.000     0.000     0.000     0.000   0.000E+00  0.00 ! Gly
+ 163.545   1.976 -5996.349  1676.896  5422.473   5.557E-13  0.00 ! Thr
+ 158.959   1.810 -8243.740  2491.600  6900.467   1.632E-11  0.00 ! Ser
+   1.582   3.601   673.244  -173.206  -646.238   4.709E-08  0.00 ! Gln
+   7.354   3.256  -485.919   112.979   530.772   9.510E-16  0.00 ! Asn
+  25.379   2.776  -729.290   168.012   800.982   2.274E-16  0.00 ! Glu
+  25.969   2.505  -711.633   167.698   761.605   8.831E-16  0.00 ! Asp
+   6.267   3.952  -176.750    35.322   222.723   1.641E-10  0.00 ! His
+   0.755   4.649     6.176    -0.945    -9.823   1.249E-13  0.00 ! Arg
+   0.001   8.312     2.122     0.132    -6.640   3.808E-11  0.00 ! Lys
+   0.000   0.000     0.000     0.000     0.000   0.000E+00  0.00 ! Pro
+   0.000   0.000     0.000     0.000     0.000   0.000E+00  0.00 ! Pro 
+   0.000   0.000     0.000     0.000     0.000   0.000E+00  0.00 ! Pro 
+   0.000   0.000     0.000     0.000     0.000   0.000E+00  0.00 ! Pro 
+   0.000   0.000     0.000     0.000     0.000   0.000E+00  0.00 ! Pro 
diff --git a/PARAM/TiO2_fin.parm b/PARAM/TiO2_fin.parm
new file mode 100644 (file)
index 0000000..c8a2d74
--- /dev/null
+++ b/PARAM/TiO2_fin.parm
@@ -0,0 +1,25 @@
+   0.058   4.710                                            0.00 ! Pep
+  0.174   4.496     2.222    -0.393    -3.104  -1.392E-12 0.0 ! Cys 
+  4.173   4.136  -143.035    28.494   180.705   1.086E-10 0.0 ! Met 
+ 10.793   4.152  -250.420    48.235   328.091   7.237E-11 0.0 ! Phe 
+  9.872   3.799  -308.062    62.468   382.714   3.262E-10 0.0 ! Ile 
+ 12.025   4.056  -448.084    90.596   559.212   2.482E-10 0.0 ! Leu 
+  3.929   3.894  -241.329    50.844   288.017   6.165E-10 0.0 ! Val 
+  0.285   5.797   738.577  -155.331  -884.672   3.662E-09 0.0 ! Trp 
+ 29.509   4.046  -648.094   126.324   840.706   1.297E-10 0.0 ! Tyr 
+  0.142   4.512     2.390    -0.478    -2.867  -3.237E-12 0.0 ! Ala 
+  0.000   0.000     0.000     0.000     0.000   0.000E+00 0.0 ! Gly 
+163.545   1.976 -5996.349  1676.896  5422.473   7.455E-07 0.0 ! Thr 
+158.959   1.810 -8243.740  2491.600  6900.467   4.040E-06 0.0 ! Ser 
+  1.582   3.601   673.244  -173.206  -646.238   4.709E-08 0.0 ! Gln 
+ 14.079   3.023  -693.399   159.850   741.239   2.726E-06 0.0 ! Asn 
+ 19.146   2.797  -579.951   133.066   639.665   1.702E-08 0.0 ! Glu 
+ 19.992   2.515  -576.973   134.999   621.292   3.119E-08 0.0 ! Asp 
+  6.267   3.952  -176.750    35.322   222.723   1.641E-10 0.0 ! His 
+  0.755   4.649     6.176    -0.945    -9.823   1.249E-13 0.0 ! Arg 
+  0.112   5.414     8.877    -1.471   -13.249  -2.915E-13 0.0 ! Lys 
+  0.000   0.000     0.000     0.000     0.000   0.000E+00 0.0 ! Pro 
+   0.000   0.000     0.000     0.000     0.000   0.000E+00  0.00 ! Pro
+   0.000   0.000     0.000     0.000     0.000   0.000E+00  0.00 ! Pro
+   0.000   0.000     0.000     0.000     0.000   0.000E+00  0.00 ! Pro
+   0.000   0.000     0.000     0.000     0.000   0.000E+00  0.00 ! Pro
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 d44e78f..c037ff3 100644 (file)
--- a/source/unres/src_MD-M/energy_p_new_barrier.F
+++ b/source/unres/src_MD-M/energy_p_new_barrier.F
@@ -12659,23 +12659,37 @@ C for vectorization reasons we will sumup at the end to avoid depenence of previ
        sc_aa_tube=sc_aa_tube_par(iti)
        sc_bb_tube=sc_bb_tube_par(iti)
        enetube(i+nres)=sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6
+C       enetube(i+nres)=0.0d0
 C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
 C now we calculate gradient
        fac=-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff-
      &       6.0d0*sc_bb_tube/rdiff6/rdiff
+C       fac=0.0
 C now direction of gg_tube vector
 C Now cavity term E=a(x+bsqrt(x)+c)/(1+dx^12)
-         if (acavtub(iti).eq.0.0d0) go to 667
+         if (acavtub(iti).eq.0.0d0) then
+C go to 667
+         enecavtube(i)=0.0
+         faccav=0.0
+         else
          denominator=(1.0+dcavtub(iti)*rdiff6*rdiff6)
          enecavtube(i)=
-     &   acavtub(iti)*(rdiff+bcavtub(iti)*sqrt(rdiff)+ccavtub(iti))
+     &   (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti))
      &   /denominator
-         faccav=(acavtub(iti)*(1.0+bcavtub(iti)/2.0/sqrt(rdiff))
-     &   *denominator-acavtub(iti)*(rdiff+bcavtub(iti)*sqrt(rdiff)
-     &   +ccavtub(iti))*rdiff6**2.0d0/rdiff*dcavtub(iti))
+C         enecavtube(i)=0.0
+         faccav=((bcavtub(iti)*1.0d0+acavtub(iti)/2.0d0/sqrt(rdiff))
+     &   *denominator-(bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)
+     &   +ccavtub(iti))*rdiff6**2.0d0/rdiff*dcavtub(iti)*12.0d0)
      &   /denominator**2.0d0
+C         faccav=0.0
          fac=fac+faccav
- 667     continue
+C 667     continue
+         endif
+         print *,"TUT",i,iti,rdiff,rdiff6,acavtub(iti),denominator,
+     &   enecavtube(i),faccav
+         print *,"licz=",
+     & (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti))
+         print *,"finene=",enetube(i+nres)+enecavtube(i)
          do j=1,3
           gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac
           gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac
@@ -12690,7 +12704,7 @@ C        if (acavtub(iti).eq.0.0) cycle
 
 
         do i=itube_start,itube_end
-          Etube=Etube+enetube(i)+enetube(i+nres)
+          Etube=Etube+enetube(i)+enetube(i+nres)+enecavtube(i)
         enddo
 C        print *,"ETUBE", etube
         return
diff --git a/source/unres/src_MD-M/parmread.F b/source/unres/src_MD-M/parmread.F
index 8fa2bad..b80095b 100644 (file)
--- a/source/unres/src_MD-M/parmread.F
+++ b/source/unres/src_MD-M/parmread.F
@@ -1369,7 +1369,8 @@ c           augm(i,j)=0.5D0**(2*expon)*aa(i,j)
       pep_bb_tube=-sigeps*4.0d0*epspeptube*sigmapeptube
       write(iout,*) pep_aa_tube,pep_bb_tube,tubetranenepep
       do i=1,ntyp
-       read(itube,*) epssctube,sigmasctube,tubetranene(i)
+       read(itube,*) epssctube,sigmasctube,acavtub(i),bcavtub(i),
+     & ccavtub(i),dcavtub(i),tubetranene(i)
        sigmasctube=sigmasctube**6
        sigeps=dsign(1.0D0,epssctube)
        epssctube=dabs(epssctube)
UNRESPACK 3.x