[gmx-users] extracting water molecules from trajectory

[Berk Hess]

>From: Kay Gottschalk <kay.gottschalk at weizmann.ac.il>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] extracting water molecules from trajectory
>Date: Wed, 19 May 2004 17:35:19 +0300
>
>thanks, works:) Would be neat to have the protein-water distance as  
>b-factor in the output-pdb - where would I have to change things to get  
>that done?

Gromacs 3.2 already does this.
It writes distances for all atoms in the solvent.
I noticed that all distances are taken with respect to the protein
atom which was found to be closest to the -da atom of each solvent
molecule. This is not necessarily the closest distance to the protein
and it is not described exactly in the description.
Maybe we should change this?

Berk.

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