[gmx-users] No. of solvent molecules around Solute

David spoel at xray.bmc.uu.se
Thu Dec 23 09:07:27 CET 2004

On Thu, 2004-12-23 at 12:18 +0530, Alok wrote:
> Dear Gmx Users,
>                              I want to calculate number of Solvent 
> Molecules around a specific atom of Solute (i.e. protein) with passes of 
> time.
check trjorder
>   I check the archive but i not found any posting related to my problem. 
> I also tried  g_sorient program but it doesnt help me.
>    i am also intrested to calcule to number of solvent molecules which 
> simultanously intract with two atoms  of solute .
> like atom1---solvent-----atom2 .
> can anyone suggesd me suitable tool for my problem.

myabe you can do it by runnnig g_hbond twice, and the second time use
the index file that it produces.

> Thanks in advance.
>         with regards,
>             Alok Jain
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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