if you only want the pdb file at a specific moment you can use -dump trjconv -f traj.xtc -s file.tpr -o pdb_at_time.pdb -dump 10
the "pdb_at_time.pdb" file will be the structure at 10 ps. You can then write a script to go through all your simulation. cheers Fra On Fri, 19 Apr 2013, at 12:16 PM, aixintiankong wrote: > Dear, > I have made a 10ns prodution MD, The set dt=0.002，nstxtcout = > 500 in mdp file. I have made 10ns prodution MD, I want to extract > frames from the molecular dynamics simulations at regular intervals > of 10ps and keep the file as individual pdb file i want to use > the follow command , > trjconv -s topol.tpr -f traj.xtc -skip (number) -o conf.pdb > -sep > but i don't now how to set the number of skip,please help me and tell me > what the skip mean > thank you ! > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Francesco frac...@myopera.com -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
