[gmx-users] Fw: -sep option
Sent from Yahoo Mail on Android - Forwarded Message - From: "Mansoureh Shahbazi" <shahbazi.2...@rocketmail.com> To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>, "Justin Lemkul" <jalem...@vt.edu> Cc: Sent: Sun, Mar 11, 2018 at 1:22 Subject: Re: [gmx-users] -sep option Dear justin, I want to make pdb files with regular intervals from a long trajectory.Can you please tell me an example command line using -sep? I want to get 100 pdbs from a 100 ns trajectory with 1ns (1000 ps) intervals. Sent from Yahoo Mail on Android On Sat, Mar 10, 2018 at 20:56, Justin Lemkul<jalem...@vt.edu> wrote: On 3/10/18 9:18 AM, Mansoureh Shahbazi wrote: > Dear colleagues, How should I use -sep option to convert a frame of a > trajectory to pdb? Can anyone send me the command line? Thanks The -sep option is used to write a given interval of a trajectory into separate files. If you just want a single frame, you should use -dump and the corresponding time in ps. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] -sep option
Dear justin, I want to make pdb files with regular intervals from a long trajectory.Can you please tell me an example command line using -sep? I want to get 100 pdbs from a 100 ns trajectory with 1ns (1000 ps) intervals. Sent from Yahoo Mail on Android On Sat, Mar 10, 2018 at 20:56, Justin Lemkul<jalem...@vt.edu> wrote: On 3/10/18 9:18 AM, Mansoureh Shahbazi wrote: > Dear colleagues, How should I use -sep option to convert a frame of a > trajectory to pdb? Can anyone send me the command line? Thanks The -sep option is used to write a given interval of a trajectory into separate files. If you just want a single frame, you should use -dump and the corresponding time in ps. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] -sep option
Dear colleagues, How should I use -sep option to convert a frame of a trajectory to pdb? Can anyone send me the command line? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fw: asking guidance
Dear director,I am using Gromacs package to perform MD simulations and I have a 100 ns long MD simulation. For the further assays, I must split this 100 ns trajectory into 100 pdb files (to get one pdf file from each 1000 ps or 1 ns of simulation). I have found two commands: gmx trjconv -s topol.tpr -f md_0_1.xtc -dt 1000 -o trj.pdb gmx trjconv –f md.xtc –s md.tpr –b 1 –e 1000 –o md.pdb (and -b 1001 -e 2000 and so on ) I tried both of them. But for the first one, I got only one pdb file and for the second command, I have to repeat the command 100 times to get them and furthermore I am not sure it gives the correct results. Can you please tell me is there any command to split the 100 ns trajectory with the time intervals of 1000 ps and get 100 pdb files at one time? If no, please make me aware that is the second command gives the true result? I am looking forward to your answer, Thanks in advance for your guidance,Sincerely yours,Mansoureh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
