[gmx-users] writing trajectory with water molecules within a distance from protein
roland at utk.edu
Mon May 9 22:10:37 CEST 2011
there is no tool to do that. Trajectories assume to have the same number of
atoms per frame. What you can do is use g_order (it gives you the water
sorted by distance and the number of water within .5nm) or g_select (it can
give you an index file with the atoms within .5nm for each frame)
On Mon, May 9, 2011 at 10:50 AM, maria goranovic
<mariagoranovic at gmail.com>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
> Maria G.
> Technical University of Denmark
> 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