[gmx-users] writing trajectory with water molecules within a distance from protein

Roland Schulz 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
> Copenhagen
> --
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