[gmx-users] WHAM
rose rahmani
rose.rhmn93 at gmail.com
Mon Dec 18 08:57:42 CET 2017
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 <nedomacho at 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 very outdated Gromacs version.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.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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