[gmx-users] Weird configuration when pulling rate is small

Erik Marklund erik.marklund at chem.ox.ac.uk
Fri Feb 12 10:42:37 CET 2016

Dear Ming,

Still, that means that your simulation is ok, or at least not broken in the way your visualisation software suggested.

Kind regards,

> 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,
> Ming
> -- 
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list