[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

-Trayder


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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


More information about the gromacs.org_gmx-users mailing list