Hi Blake, Centering on the solute should help.
Cheers, Tsjerk On Sat, Nov 2, 2013 at 3:55 PM, rankinb <rank...@purdue.edu> wrote: > Hi all, > > I am trying to use trjconv to remove PBC. More specifically, I would like > to extract the coordinates of all the water molecules within a certain > distance of a single solute molecule. However, I have been unsuccessful in > doing so, even after following the guidelines on the GROMACS website > ( > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > ). > > Here are some of the things I have tried. First, I extracted the indices of > the water molecules of interest using g_select and used trjconv to extract > the coordinates from the .gro file. Then I used trjconv -pbc mol on the > resulting .gro file. The problem is that some of the water molecules are > on > opposite sides of the box. > > Does anyone have any suggestions? > > Thank you very much, > Blake > > PhD Candidate > Purdue University > Ben-Amotz Lab > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/trjconv-for-pbc-tp5012160.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists