[gmx-users] Weird configuration when pulling rate is small
erik.marklund at chem.ox.ac.uk
Fri Feb 12 10:42:37 CET 2016
Still, that means that your simulation is ok, or at least not broken in the way your visualisation software suggested.
> On 12 Feb 2016, at 06:51, Ming Tang <m21.tang at qut.edu.au> wrote:
> Dear Erik,
> Thanks for your advice. I think you are right. However, when using -pbc whole, every chain is intact but the three chains separate in some frames; when using -pbc nojump, the collagen molecule is not intact (there is a small part stay in the other box ) either. If I fix one end, and use -pbc whole, the problem is fixed.
> Thanks and regards,
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