[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken

[Justin A. Lemkul]

On 1/9/10 10:42 PM, Chih-Ying Lin wrote:
> Hi
> I did the EM and the potential energy went to the very negative number.
> But the simulaiton broke in the PR step.
> Thank you
> Lin
>

Saying the system broke is useless.  There will certainly be some information in 
the .log file (LINCS warnings, etc).  If that is the case, then you need to 
follow the standard advice that is always given in such cases:

http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

If you want more detailed advice, provide real output - information from how 
well the EM converged, messages in the .log file (unless it's just LINCS stuff, 
see the above links).  Also realize that EM does not always remove all 
potentially problematic contacts.  Your system may require a bit more finesse.

-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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