[gmx-users] Detection of Internal water along MD trajectory

Trayder Thomas trayder.thomas at monash.edu
Wed Mar 19 01:33:32 CET 2014

If you can think of a sensible way to define your area of interest, a
simple VMD script can count waters:
[atomselect <mol ID> "name \"O.*\" and resname <water resname> and same
residue as <define area somehow>" frame <frame>] num

e.g. To count the number of water molecules within 5A of residues 1-5:
[atomselect 0 "name \"O.*\" and resname SOL and same residue as within 5 of
resid 1 2 3 4 5" frame now] num


On Mon, Mar 17, 2014 at 8:13 PM, James Starlight <jmsstarlight at gmail.com>wrote:

> Dear Gromacs users!
> I've performed md simulation of water soluble protein having
> water-assessable channel in its interior. I'd like to perform analysis
> of average number of water molecules detected within the protein
> interior during MD trajectory with the possible visualization of such
> internal water binding sites. Does SASA calculation which I've seen in
> vmd could provide me with additional insights? I'd be thankful if you
> provide me with some Gromacs or VMD tools suitable for such task.
> Many thanks for help,
> James
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