A work around will be available in the future as a plugin for VMD. For your reference read these threads:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/14140.html http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/13217.html On 10 May 2011 03:12, Roland Schulz <rol...@utk.edu> wrote: > > > On Mon, May 9, 2011 at 6:28 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > >> On 10/05/2011 12:50 AM, maria goranovic wrote: >> >>> Dear experts >>> >>> I have a protein simulation in a water box. I now want to write a >>> trajectory containing only the protein, and water molecules within 5 >>> Angstroms of the protein, with the water list being updated each time step. >>> How can one do this? Appreciate the help >>> >> >> g_select is useful for "dynamic" selections of this type. g_select -select >> "help" can give examples and such. >> >> I'd hope it's been designed so that then using trjconv to extract such >> selections works, but I can't think how, having not ever tried. >> > g_select writes out one index group per time frame. But trjconv can't use a > different index group for each frame. Thus it can't be used to write out a > trajectory with those atoms for each frame. Part of the problem is that the > trajectory format doesn't support different number of atoms for different > frames. > What is possible is writing a small script around trjconv to produce one > gro/trr file per frame with only those atoms. > > Roland > > >> Mark >> -- >> 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 >> >> >> > > > -- > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov > 865-241-1537, ORNL PO BOX 2008 MS6309 > > -- > 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 > -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/
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