[gmx-users] pbc

David spoel at xray.bmc.uu.se
Thu Jul 1 20:34:21 CEST 2004

On Thu, 2004-07-01 at 18:38, Bruno Pagano wrote:
> Hi,
> I am trying to get a continuous trajectory centered in the box with a whole
> molecule...
> shouldn't be that difficult....
> but whatever I try I do not manage.
How about trjconv -fit ?
> I have a whole starting structure, I can get first a whole trajectory, then I
> run nojump, then I would like to center that but all the atoms diffuse out of
> the box...
No jump means remove the pbc IIRC.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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