[gmx-users] position restraints crashing

[Steffen Wolf]

Alan Dodd wrote:
> No, minimisation was without PR.  Surely minimisation
> with PR would *increase* bad contacts, rather than
> removing them?  I've tried running for a while under
> normal MD, successfully and without LINCS errors, then
> taking the endpoint and running under PR, but it still
> crashes almost instantaneously, so it's unlikely to
> just be a matter of energies or bad contacts, I'd have
> thought?
>
>   
Yes, so it looks that minimization ended at a metastable point, which 
was surmounted by a free MD run but kept by the PR and therefore caused 
the system to crash. Which minimization algorithm did you use? Steep or CG?

-- 
Dipl.-Chem. Steffen Wolf
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany
Tel: +49 (0)234 32 28363
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E-Mail: swolf at bph.rub.de
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