Dear, gmx-users, Hello everyone, I'm simulating a peptide in an SDS micelle. The simulation was performed for 100ns When I view the trajectory in VMD, a portion of the SDS micelle moves to the right and goes into the next box. Of course, because of periodic boundary conditions. I tried using trjconv to see if I could suppress the periodic boundary conditions for the purpose of visualization. I've used all the different -pbc options none of them helped.
options i have used trjconv -f .trr -s .tpr -o nojump.trr -pbc nojump used the above created nojump.trr in the below command trjconv -f nojump.trr -s .tpr -n .ndx -o .trr -b 0 -e 100000 -ur compact -pbc mol -center Selected Protein&sds as centering group and system as output group Any suggestions on how to go about doing this? Thanks, Sanket -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
