Re: [gmx-users] how to extract individual frames from trajectory
On 4/19/13 8:03 AM, aixintiankong wrote: At 2013-04-14 11:07:39,aixintiankong wrote: Dear, I have made a 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. The dt=0.002，nstxtcout = 500，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. Your .mdp settings suggest that you have saved frames every 0.1 ps. Confirm with gmxcheck. If you have frames every 1 ps and want output every 10 ps, then 10/1 = 10 for the value of -skip. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
[gmx-users] how to extract individual frames from trajectory
At 2013-04-14 11:07:39,aixintiankong wrote: Dear, I have made a 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. The dt=0.002，nstxtcout = 500，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. thank you ! -- gmx-users mailing listgmx-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
Re: [gmx-users] how to extract individual frames from trajectory
On 4/13/13 11:07 PM, aixintiankong wrote: Dear, I have made a 75ns 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 get many individual pdb files. colud anyone can tell me how to perform the command? trjconv and some iteration or combination of -skip, -sep, and/or -dump will do the trick. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
[gmx-users] how to extract individual frames from trajectory
Dear, I have made a 75ns 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 get many individual pdb files. colud anyone can tell me how to perform the command? thank you ! -- gmx-users mailing listgmx-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
