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