What you will do if you don't have a responsible professor? I tried to install GROMACS in my computer vmware>Ubuntu>... but it wasn't successful and I couldn't.Anyway, you're right I shouldn't discuss these problems here. Thanks again -Rose
Sent from my iPhone > On Dec 18, 2017, at 11:58, Alex <nedoma...@gmail.com> wrote: > >> On 12/18/2017 1:14 AM, João Henriques wrote: >> First, you don't need "special computers" to run or compile gromacs. It >> helps to have multiple compute nodes at your disposal, but it isn't a >> requirement *per se*. Also, you don't need to be root to compile your own >> gromacs installation. You can indeed install your own gromacs version on >> the cluster you use to run your simulations. > Well, I do need "special computers" to run GMX. :) > Jokes aside, this is a solid point -- even if one uses a Windows machine, > virtualbox+linux+gromacs is always useful to tinker at home for when you have > no access to the "special computer." That, or cygwin, although that thing > nauseates me. > > Rose, if you are a student, it would be a good idea to ask for better > instruction from your professors. This board is quite limited in replacing > the kind of instruction you may need. Three months is actually a reasonable > amount of time to get the basics of MD and Gromacs right. Without those > basics, it is completely pointless to try doing any work. > > Alex > > >> >>> On Mon, Dec 18, 2017 at 8:57 AM, rose rahmani <rose.rhm...@gmail.com> wrote: >>> >>> 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? 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