Ohhh...! :-) I could not get it on my own independently! Thanks for all your explanation! Many many thanks.
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Tuesday, March 26, 2013 12:02 AM Subject: Re: [gmx-users] position restraints On 3/25/13 3:25 PM, Shima Arasteh wrote: > Dear Justin, > > As I got, I need to edit the lipid_posre.itp file. To do so, I need to change > numbering of position restraining in lipid_posre.itp file to what they are in > their original itp file: In my case popc.itp file. > Am I right? > More or less, but for the sake of clarity, let me explain this fully so you can hopefully arrive at a resolution quickly. Say I have a system of arbitrary molecules that have 4 atoms each. Position restraints only work per [moleculetype], so using genrestr is somewhat dangerous unless you are working with a coordinate file or suitable index file that only specifies a single molecule. Otherwise, the selection is rather ham-handed and actually gives you a nonfunctional .itp file (hence the WARNING in the help description). Therefore, I can only use atom numbers 1, 2, 3, and 4 in my [position_restraints] directive. Anything above 4 (i.e. based on selecting multiple molecules in genrestr) triggers a fatal error. What then happens is that grompp reads those atoms, and every time it encounters those atom numbers within the [moleculetype] (irrespective of how many times that molecule appears), restraints are applied as specified. So, if you want to restrain only P atoms of every POPC molecule, you basically need a one-line .itp file. If, for instance, P is atom number 8: [ position_restraints ] 8 1 0 0 1000 That will restrain all P atoms (every time they occur, as grompp finds them throughout the coordinate file) in the z-dimension only. Hopefully that all makes sense and this experience has been educational as far as how these things work. -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 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 -- 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
