> Hi all, > I am trying to use *trjconv command for -pbc but POPC molecules are > breaking > when visualize in VMD. The commands used are > grompp -f pr.mdp -c em_out.gro -p .top -n index.ndx -o out.tpr > trjconv -f em_out.gro -s out.tpr -o trj_out.gro -pbc inbox or cluster > or > whole > Thi trj_out.gro contain broken POPC molecules
GROMACS doesn't ever write molecules that are broken across periodic boundaries. Thus either you've introduced a visual artefact with your use of VMD, or your EM produced a broken molecule through using a broken physical model. You should examine the nature of "broken", and/or try using ngmx to confirm what is really going on. Your grompp-trjconv sequence is not necessary for massaging the PBC behaviour of your EM output. trjconv will accept a .gro file for the -s flag, which you will see is indicated in the section of the output of "trjconv -h" that deals with the -s flag. This is quite general GROMACS behaviour. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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
