Why you don't answer me?is there anything wrong in my question? Thank you Sent from my iPhone
> On Dec 17, 2017, at 17:36, rose rahmani <rose.rhm...@gmail.com> wrote: > > Hi, > > I try to use umbrella sampling for calculating PMF. i change distance > between protein and ZNS nanosheet. I use gomacsV4.5.4 > > after minimization and equilibration. i use: > > grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -o pull.tpr > > this is md_pull.mdp: > > integrator = md > dt = 0.002 > nsteps = 1000000 > nstxout = 5000 > nstvout = 5000 > nstfout = 500 > nstlog = 500 > nstenergy = 1000 > nstxtcout = 1000 > nstlist = 10 > rlist = 1.5 > coulombtype = pme > rcoulomb = 1.5 > vdwtype = Switch > rvdw_switch = 1.0 > rvdw = 1.2 > pcoupl = no > gen_vel = no > constraints = h-bonds > ns_type = grid > pbc = xy > freezegrps = WAL ZnS > freezedim = Y Y Y Y Y Y > energygrp-excl = WAL WAL ZnS ZnS > energygrps = SOL WAL ZnS Protein NA CL > nwall = 2 > wall-atomtype = C C > wall-type = 9-3 > wall-density = 150 150 > wall-ewald-zfac = 3 > ewald-geometry = 3dc > fourierspacing = 0.12 > tcoupl = v-rescale > tc-grps = System > tau-t = 0.1 > ref-t = 300 > > ; Pull code > pull = umbrella > pull_ngroups = 1 > pull_group0 = ZnS > pull_group1 = Protein > pull_geometry = direction > pull_vec1 = 0 0 1 > pull_dim = N N Y > pull_rate1 = -0.01 > pull_k1 = 5000 > pull_start = yes > pull_nstxout = 50 > > then: mdrun -s pull.tpr > then:trjconv -s pull.tpr -f traj_comp.xtc -o conf.gro -sep > > i got 1000 configuration, i selected 27 of them and foe each of them i run > md_umbrella.mdp > > for example: grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top > -n index.ndx -o umbrella0.tpr and then: > > mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg > > > .This is md_umbrella.mdp file: > > ntegrator = md > dt = 0.002 > nsteps = 2000000 > nstxout = 5000 > nstvout = 5000 > nstfout = 500 > nstlog = 500 > nstenergy = 1000 > nstxtcout = 1000 > nstlist = 10 > rlist = 1.5 > coulombtype = pme > rcoulomb = 1.5 > vdwtype = Switch > rvdw_switch = 1.0 > rvdw = 1.2 > pcoupl = no > gen_vel = no > constraints = h-bonds > ns_type = grid > pbc = xy > freezegrps = WAL ZnS > freezedim = Y Y Y Y Y Y > energygrp-excl = WAL WAL ZnS ZnS > energygrps = SOL WAL ZnS Protein NA CL > nwall = 2 > wall-atomtype = C C > wall-type = 9-3 > wall-density = 150 150 > wall-ewald-zfac = 3 > ewald-geometry = 3dc > fourierspacing = 0.12 > tcoupl = v-rescale > tc-grps = System > tau-t = 0.1 > ref-t = 300 > > pull = umbrella > pull_ngroups = 1 > pull_group0 = ZnS > pull_group1 = Protein > pull_geometry = direction > pull_vec1 = 0 0 1 > pull_dim = N N Y > pull_rate1 = 0.0 ; 1 nm per ns > pull_k1 = 5000 > pull_start = yes > pull_nstxout = 50 > ........................................................... > > then i use : > > wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal > > > i get histo.xvg and profile.xvg file but the profile.xvg contains nan > vavlue. i don't know why? > > > # This file was created Wed Dec 13 14:54:35 2017 # by the following > command: # g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal > # # g_wham is part of G R O M A C S: # # GROwing Monsters And Cloning > Shrimps # @ title "Umbrella potential" @ xaxis label "z" @ yaxis label "E > (kcal mol\S-1\N)" @TYPE xy 5.723834e-01 -nan 6.714198e-01 -nan 7.704562e-01 > -nan 8.694925e-01 -nan 9.685289e-01 -nan 1.067565e+00 -nan 1.166602e+00 > -nan 1.265638e+00 -nan > > . > > . > > . > > . > > > Would you please help me? i have not encounter this problem before > > and also i want protein get closer to ZnS sheet during pulling in just > Z direction and straightforward to sheet( like one straight line to > sheet), is this suitable md_pull.mdp file for this approach? and what > about time?is 4nS suitable for each window?is it possible at all? > > Would you please help me? > > > Best regards > > Rose > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
