[gmx-users] Check for bad contacts and/or reduce the timestep

[Justin A. Lemkul]

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 better.

-Justin

> Thanks alot of for help.
> 
> -Nisha
> 
> 
> 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
>>
>> -- 
>> ========================================
>>
>> 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
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================