Dear all, Is it possible to add connectivity information in the trajectory file? I'm dealing with CG MD using Martini FF. After the production run, I checked my trajectory by loading the full.gro and full.trr in VMD. However, I could see nothing but a stack of CG beads moving around. No bonds there.
It was mentioned that (maybe in the revision history, I couldn't find it any more as gromacs is moving to a new site) Gromacs 4.0.5 is able to add connectivity information in the trajectory file, which is very helpful in CG simulation. I got one trajectory file in pdb format by trying the following command: Trjconv -f full.trr -s full.tpr -n index.ndx -o test.pdb I checked the test.pdb(with many frames) and found no connectivity information. How could I add connectivity information in the trajectory file? Any suggestions are greatly appreciated! Many thanks in advance!! Yours, Chuan Liao
_______________________________________________ gmx-users mailing list [email protected] http://lists.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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
