hello everybody I have simulated DNA using CHARMM force field for 50 ns with 2 ps snapshots for each step. when I wanted to convert .xtc trajectory files to .pdb using trjconv, some of the snapshots were collaborated. I have used periodic boundary conditions in this simulations. To convert, I used bellow command:
trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -center In collaborated .pdb files two strands of DNA separated from each other. when I used bellow command instead of above command, this collaborated .pdb file will be corrected, but some of the other .pdb files will be ruined as same as trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol would you please help me to solve this technical problem? I am looking forward hearing of you, Mehdi Bagher Poor -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
