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

[Justin A. Lemkul]

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

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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

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