[gmx-users] WHAM
Rose
rose.rhmn93 at gmail.com
Mon Dec 18 09:48:28 CET 2017
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 <nedomacho at 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.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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