[gmx-users] Re: Can you help me?
feenstra at few.vu.nl
Thu Apr 13 09:36:02 CEST 2006
Dr. Dong XY wrote:
> Hello, K. Anton Feenstra
> I'm a student of Tianjin University of China. I want to get the chemical
> unfolding structure of protein.But I can't minimize the mixture. I always get the
> following cues:
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1000
> I try so many ways, but they doesn't waork. Can you tell me what did you do?
> Thank you in advance and best wishes!
This is not necessarily a problem. You should look at the final energy.
Is it low enough? Also, you can look at the separate energy terms, like
angles, dihedrals, Lennard-Jones, and so. You can find these in the
logfile from mdrun (usually 'md.log').
* NOTE: New Affiliation, Phone & Fax numbers (below) *
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 |
| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" (RHCP) |
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