From 4d4be87fb43102a6a5be442699a953ef327ecbde Mon Sep 17 00:00:00 2001 From: Adam Sieradzan Date: Thu, 26 Jan 2017 13:43:48 +0100 Subject: [PATCH] nanophere working --- PARAM/TiO2.parm | 26 +++++++++++++++++++++++- PARAM/TiO2_fin.parm | 25 +++++++++++++++++++++++ source/unres/src_MD-M/energy_p_new_barrier.F | 28 +++++++++++++++++++------- source/unres/src_MD-M/parmread.F | 3 ++- 4 files changed, 73 insertions(+), 9 deletions(-) create mode 100644 PARAM/TiO2_fin.parm diff --git a/PARAM/TiO2.parm b/PARAM/TiO2.parm index e236309..cb975e5 100644 --- 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 2 4.173 4.136 -143.035 28.494 180.705 1.086E-10 ! Met 1 10.793 4.152 -250.420 48.235 328.091 7.237E-11 ! Phe 2 9.872 3.799 -308.062 62.468 382.714 3.262E-10 ! Ile 2 12.025 4.056 -448.084 90.596 559.212 2.482E-10 ! Leu 1 3.929 3.894 -241.329 50.844 288.017 6.165E-10 ! Val 2 0.285 5.797 738.577 -155.331 -884.672 3.662E-09 ! Trp 1 29.509 4.046 -648.094 126.324 840.706 1.297E-10 ! Tyr 1 0.058 4.710 0.612 -0.108 -0.790 -3.640E-14 ! Ala 0 0.000 0.000 0.000 0.000 0.000 0.000E+00 ! Gly 1 163.545 1.976 -5996.349 1676.896 5422.473 5.557E-13 ! Thr 1 158.959 1.810 -8243.740 2491.600 6900.467 1.632E-11 ! Ser 3 1.582 3.601 673.244 -173.206 -646.238 4.709E-08 ! Gln 1 7.354 3.256 -485.919 112.979 530.772 9.510E-16 ! Asn 3 25.379 2.776 -729.290 168.012 800.982 2.274E-16 ! Glu 1 25.969 2.505 -711.633 167.698 761.605 8.831E-16 ! Asp 1 6.267 3.952 -176.750 35.322 222.723 1.641E-10 ! His 3 0.755 4.649 6.176 -0.945 -9.823 1.249E-13 ! Arg 3 0.001 8.312 2.122 0.132 -6.640 3.808E-11 ! Lys 1 0.000 0.000 0.000 0.000 0.000 0.000E+00 ! Pro \ 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 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 --- 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 --- 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) -- 1.7.9.5