Dear All First I ran a 5 ns MD (md-0ns-5ns), I get md-0ns-5ns.tpr and md-0ns-5ns.cpt,then I extend it for 1 ns by
tpbconv -s tpbconv -s md-0ns-5ns.tpr -extend 1000 -o md-5ns-to-6ns.tpr mdrun -deffnm md-5ns-to-6ns -cpi md-0ns-5n.cpt Then I further extend it for 2 ns by tpbconv -s md-5ns-to-6ns.tpr -extend 2000 -o md-6ns-to-8ns.tpr mdrun -deffnm md-6ns-to-8ns -cpi md-5ns-to-6ns.cpt Then I connect all the above 3 MDs together. First I connect the first 2: trjcat -f md-0ns-5ns.trr md-5ns-to-6ns.trr -o md-0ns-6ns.trr Then I connect the output md-0ns-6ns.trr with md-6ns-to-8ns.trr by trjcat -f md-0ns-6ns.trr md-6ns-to-8ns.trr -o md-0ns-8ns.trr Now I want to extract the PDB files at different time intervals from md-0ns-8ns.trr. If I extract the PDB from md-0ns-8ns.trr at 1 ns, I can use the following command I think: trjconv -f md-0ns-8ns.trr -s md-0ns-5ns.tpr -o md-0ns-8ns_extracted_at_1ns.pdb -dump 1000. Here is my question. If I want to extract the PDB from md-0ns-8ns.trr at 7 ns, should I use the command trjconv -f md-0ns-8ns.trr -s md-0ns-5ns.tpr -o md-0ns-8ns_extracted_at_7ns.pdb -dump 7000, or should I use the following command trjconv -f md-0ns-8ns.trr -s md-5ns-to-6ns.tpr -o md-0ns-8ns_extracted_at_7ns.pdb -dump 7000 I am looking forward to getting your reply. Cheers, Acoot -- 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
