Quoting sudheer babu <[EMAIL PROTECTED]>: > 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
Your scheme will not work because the structure in the .tpr file is the same as in your em_out.gro, which you claim to be broken. I'm assuming em_out.gro refers to your structure following energy-minimization? And if so, I'm wondering what you've done that's left a broken molecule following EM. Is your em_out.gro whole? -Justin > Thi trj_out.gro contain broken POPC molecules > Pls suggest me what options I have to use for -pbc? or any addition option I > have to use? > Thanks in advance....... > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ 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