[gmx-users] how to extract trajectories into individual pdb file?
hello: I've finished a MD job and I am wondering how can we extract individual pdb from trajectories in Gromacs? each time I always get a single pdb contains lots of snapshots. thank you very much best Albert -- 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 trajectories into individual pdb file?
On 4/05/2012 1:10 AM, Albert wrote: hello: I've finished a MD job and I am wondering how can we extract individual pdb from trajectories in Gromacs? each time I always get a single pdb contains lots of snapshots. See trjconv -h Mark -- 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 trajectories into individual pdb file?
In particular, look at the option -sep 2012/5/3 Mark Abraham mark.abra...@anu.edu.au On 4/05/2012 1:10 AM, Albert wrote: hello: I've finished a MD job and I am wondering how can we extract individual pdb from trajectories in Gromacs? each time I always get a single pdb contains lots of snapshots. See trjconv -h Mark -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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 trajectories into individual pdb file?
On 05/03/2012 05:12 PM, francesco oteri wrote: In particular, look at the option -sep thank you for kind reply. but how to superimposed the left snapshot with the first one? thanks again for helps -- 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 trajectories into individual pdb file?
-fit 2012/5/3 Albert mailmd2...@gmail.com On 05/03/2012 05:12 PM, francesco oteri wrote: In particular, look at the option -sep thank you for kind reply. but how to superimposed the left snapshot with the first one? thanks again for helps -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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 trajectories into individual pdb file?
thank you very much. I found a problem : there is no option to select step. eg: I would like to export one snapshot at each 10ps, I don't find such kind of options.. THX On 05/03/2012 05:21 PM, francesco oteri wrote: -fit 2012/5/3 Albert mailmd2...@gmail.com mailto:mailmd2...@gmail.com On 05/03/2012 05:12 PM, francesco oteri wrote: In particular, look at the option -sep thank you for kind reply. but how to superimposed the left snapshot with the first one? thanks again for helps -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- 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 trajectories into individual pdb file?
On 5/3/12 11:58 AM, Albert wrote: thank you very much. I found a problem : there is no option to select step. eg: I would like to export one snapshot at each 10ps, I don't find such kind of options.. That's what you can use -skip or -dt for. Alternatively, dump out frames at specific times with -dump. Note that you can find all of this, and more, in the help info printed by trjconv, as Mark originally suggested. -Justin THX On 05/03/2012 05:21 PM, francesco oteri wrote: -fit 2012/5/3 Albert mailmd2...@gmail.com mailto:mailmd2...@gmail.com On 05/03/2012 05:12 PM, francesco oteri wrote: In particular, look at the option -sep thank you for kind reply. but how to superimposed the left snapshot with the first one? thanks again for helps -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
