[gmx-users] WHAM
Alex
nedomacho at gmail.com
Sun Dec 17 22:22:54 CET 2017
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you are using a very outdated Gromacs version.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 wildly outdated (and unsupported, as I warned you) versions of the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.rhmn93 at 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
>
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