[gmx-users] Problem with CGMD

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 30 15:53:33 CET 2009

Anirban Ghosh wrote:
> Hello Justin,
> Thanx for the reply
> I tried with dt=0.02 and also with dt=0.01. but still its crashing. It 
> is crashing in the very first step. So nothings there in trr file.
> Are the options given in the MDP file correct? Actually my EM ran quite 
> well. Please advice.

If your system is collapsing at the very first step, I would argue that EM was 
not complete.  What potential energy and maximum force did you achieve?

If the .mdp file came from the MARTINI group, I would think it is appropriate; I 
have only done limited testing and found that I needed to change dt to get a 
stable simulation.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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