________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of lina [lina.lastn...@gmail.com] Sent: Thursday, October 27, 2011 10:47 AM To: Discussion list for GROMACS users Subject: [gmx-users] trjconv and -pbc
Hi, I have a problem using trjconv_g -pbc nojump or trjconv_g -pbc nojump -center I even tried the -pbc whole. The system is protein with a small molecular, for the first time period, when I checked on pymol. they are together, but later they apart, after show cell, protein inside the cell, while this small molecular outside, I did not meet such issue before, it's used to be easy to fix the pbc problem, but not this one. a bit surprise, They are supposed to be together, Thanks for any advice, I am sure it will help. Follow the workflow! http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions?highlight=pbc Just use the trjconv -h to see each option. Jan =========================================================== Jan Marzinek PhD Candidate Centre for Process Systems Engineering Department of Chemical Engineering Imperial College London South Kensington Campus London SW7 2AZ E: j.marzine...@imperial.ac.uk M: +44(0)7411 640 552 -- 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-- 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