[gmx-users] trjconv behaving differently in 3.3.3 vs previous versions

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 7 07:42:41 CET 2008

rob yang wrote:
> Hi list,
> I have a system solvated in dodecahedron box. To visualize it, I used:
> trjconv -f system.gro -s system.gro -o visual.pdb -ur compact -pbc whole
> Version 3.3.3 gave me a cubic box with broken molecules while the previous versions gave me the right visualization on the same system.gro
try -pbc mol.
otherwsie you are welcome to submit a bugzilla.

> Does anybody have any similar experiences? Thanks.
> -Rob
> _________________________________________________________________
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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://folding.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list