So, one can probably do this using a simple script? for each frame
make index file of water molecules within 0.5 nm using g_select extract frame based on above selection done concatenate frames The only problem with the above would be that the number of water molecules selected might change with each frame. Is there a way of choosing the closest, say, 1000 water molecules using g_select On Tue, May 10, 2011 at 12:28 AM, 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. > > 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 > -- Maria G. Technical University of Denmark Copenhagen
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