[gmx-users] Problem with CGMD
x.periole at rug.nl
Sat Oct 31 11:23:25 CET 2009
On Oct 30, 2009, at 3:53 PM, Justin A. Lemkul wrote:
> 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.
It may help to start with a small time step (0.001 ps) for a little
while and then switch to
longer time step 0.020 ps. This serves as equilibration of the mapped
system to the
> 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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