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
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