Mol is not a pbc's option. I want to remove PBC because, during the simulation, the protein to get close to the border of the box. This effect generate any consequence when I observe the trajectories using the software VMD. Moreover the distances protein-water are wrong. Thanks for the helps. > > > alessandro.maior...@roma2.infn.it wrote: >> Hi all, >> >> what can I remove the PBC using trjconv? I used the following command: >> >> trjconv_d -f traj.trr -s topol.tpr -pbc nojump > > I've had pretty good success using: > > trjconv -pbc mol -ur compact > > -Justin > >> >> Thanks >> _______________________________________________ >> gmx-users mailing list gmx-users@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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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