On Fri, Oct 28, 2011 at 11:47 AM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 28/10/2011 2:39 PM, lina wrote: >> >> On Thu, Oct 27, 2011 at 6:11 PM, Marzinek, Jan >> <j.marzine...@imperial.ac.uk> wrote: >>> >>> ________________________________________ >>> 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. >> >> Ha, I think I have tried those options. That's why I am confused. >> >> Thanks, > > Well, you need to try them better :) If you want your trajectory to keep > protein and something else together, you will need an index group that > combines them not jumping, and then combines them centering (or whatever).
Thanks. I did use the index group on trjconv to output the pdb of the protein and the small molecular. > > Mark > -- > 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
