You can construct such a subset after the fact by using trjconv with (say) an index group created with g_select, but you will have to script that process frame by frame yourself.
Mark On Fri, Jan 4, 2013 at 9:35 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/4/13 11:09 AM, Shima Arasteh wrote: > >> Dear users, >> >> I'm simulating a system of protein/water/popc/ions. The peptide is >> inserted through the transmembrane, and the peptide acts as a channel. >> In order to reduce the trajectory storage volume, I need to use xtc-grps >> in .mdp file. In my system, I'd rather to store the positions of >> peptide,ions and waters "near" the peptide (I mean a specific region near >> the peptide: entrances of peptide + through the peptide).The large amount >> of water molecules positions exist up and down the bilayer, are not >> expected to be saved. >> I'm wondering if it is possible to chose a specific region in xtc-groups? >> Or any other solution to reduce the storage volume of trr file? >> >> > I doubt you can achieve such a group consistently. Water molecules will > diffuse over time. Index groups provided to grompp can only be specified > to be a fixed size and cannot be dynamically created to satisfy any > geometric criterion during mdrun. Thus, your initial group may indeed > represent the desired molecules, but over time, the waters within the group > will (likely) drift away and may not be anywhere near the original position. > > If your system contains a lot of water that you deem unnecessary, perhaps > you should consider the manner in which the system was constructed... > > The only way to decrease the size of a .trr file is to decrease nstxout, > nstvout, and/or nstfout. For various technical reasons, there is no way to > save only a subset of atoms in .trr format. Refer to previous discussions > on this topic. > > -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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
