[gmx-users] WHAM

Alex nedomacho at gmail.com
Mon Dec 18 09:28:29 CET 2017


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.rhmn93 at 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 <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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