Dear Justin,I don't have special computers to be compatible with these softwares and run complex calculations.So i have to connect to some computers which is not mine and the old version is installed there.i can't update them because i'm just a normal user and not a root one! So there are two choices; not using GROMACS at all OR be convinced with the old versions. i choose latter! WHO don't like an upgraded software sir?! you are not talking with a headstrong person ;) i like to use V.2018 but it's not possible for me, i hope you understand me.💜Just this! You are talking with 3 months experienced student without any experience in any similar simulation software before!
I agree with you Alex he is a modest person ;) I understand sometimes it's not possible to say what the problem exactly is, but i ask to know if you had these problems before how did you solve it in your system, yes maybe it couldn't be the right answer for another's system but maybe a clue for someone! You have helped me many times and i really appreciate you for your attentions and kindness Thank you again dear Justin and Alex Best regards -Rose On Mon, Dec 18, 2017 at 12:52 AM, Alex <nedoma...@gmail.com> wrote: > Rose, > > Although in my opinion Justin does know everything, the problem is with > your question. You've posted the same thing over and over (and over), and > noone replied -- this could be an indicator that people simply have nothing > to say. We don't know anything about your system, we don't know whether it > is stable, what is its dynamics, etc, etc. On top of this, you are using a > very outdated Gromacs version. > > From my own experience with all versions above 5.0.x, pull in Gromacs does > work well, as long as your system behaves as expected without pulling, and, > once that has been confirmed, you use a properly selected set of pull > parameters. There are basic procedures for checking your system _prior to_ > production simulations involving external stimuli (fields, pulling, etc) -- > please follow them. And please, Please be mindful of what this message > board is, and especially of what it is not. > > Good luck! > > Alex > > > > On 12/17/2017 1:44 PM, Justin Lemkul wrote: > >> >> >> On 12/17/17 3:39 PM, Rose wrote: >> >>> Why you don't answer me?is there anything wrong in my question? >>> >> >> Contrary to popular opinion, I don't know everything :) If I don't reply >> to a question, it is because I have nothing useful to contribute. >> >> But since you asked, diagnosing what appears to be buggy behavior in >> wildly outdated (and unsupported, as I warned you) versions of the code is >> not a wise use of time. Upgrade to the latest version and try again. >> >> -Justin >> >> 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.
