[gmx-users] Check for bad contacts and/or reduce the timestep
nishap.patel at utoronto.ca
nishap.patel at utoronto.ca
Wed Dec 16 20:02:21 CET 2009
You are right, I had to delete some water molecules, it is working fine now.
Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> nishap.patel at utoronto.ca wrote:
>> Hi Justin,
>> I am trying to plot rdf of one methane molecule in water (spc
>> water, 1095(water molecule in my file). I did create the file using
>> genbox (31.010 31.010 31.010). This is the energy minimization
>> file I am using:
> Surely a 31-nm cubic box is excessive for a system of 1095 water
> molecules. You are aware that Gromacs specifies all units in nm, not
> Angstrom, right?
> As for the parameters in the .mdp file, I don't see anything that would
> necessarily cause the instability you're seeing. A better coulombtype
> method (in general) is PME, but this may not have a significant effect
> during the EM procedure.
>> title = Methane in water
>> cpp = /lib/cpp
>> include = -I../top
>> integrator = steep
>> emtol = 1.0
>> nsteps = 100
>> nstenergy = 10
>> nstxtcout = 10
>> xtc_grps = CH4 SOL
>> energygrps = CH4 SOL
>> nstlist = 5
>> ns_type = simple
>> rlist = 1.0
>> coulombtype = cut-off
>> rcoulomb = 1.0
>> rvdw = 1.0
>> constraints = none
>> pbc = no
>> I tried reducing the steps (to 9 instead of 100) and it works but
>> it doesn't make sense. I am going to try to build the system again.
> Reducing the number of steps will actually make the energy minimization
> worse! If anything, use *more* steps to try to make the structure
>> Thanks alot of for help.
>> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>>> nishap.patel at utoronto.ca wrote:
>>>> Hi, I tried energy minimization and I am getting the error while
>>>> I am running the minimization step. But then I still tried to
>>>> carry on with normal md-simulation, and it was fine, but I am
>>>> sure it won't give me the result that it should. Is there a
>>>> reason for that? I have tried very low energy steps as well, but
>>>> I am still getting the error.
>>> If minimization still reports the same problems, then what I said
>>> before is still true - you have bad contacts somewhere. Have you
>>> looked at the trajectory to see where these problematic atoms are and
>>> what might be causing the clashes?
>>> Sometimes running sufficiently gentle equilibration can relax away some
>>> of these bad contacts, but that is rarely the case and often problems
>>> will manifest later on in the course of MD. I would seriously consider
>>> re-evaluating however you built your system (which you haven't told us)
>>> and try to get the energy minimization to actually work before just
>>> plowing ahead with fingers crossed.
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> gmx-users mailing list gmx-users at gromacs.org
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> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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