[gmx-users] writing trajectory with water molecules within a distance from protein
roland at utk.edu
Tue May 10 02:12:13 CEST 2011
On Mon, May 9, 2011 at 6:28 PM, Mark Abraham <Mark.Abraham at 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
What is possible is writing a small script around trjconv to produce one
gro/trr file per frame with only those atoms.
> gmx-users mailing list gmx-users at gromacs.org
> 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-request at 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
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users