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
Fax: +49 (0)234 32 14626
E-Mail: [EMAIL PROTECTED]
Web: http://www.bph.rub.de
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