[gmx-users] calculating electrostatic potential

Justin A. Lemkul jalemkul at vt.edu
Sun May 15 21:47:23 CEST 2011

delara aghaie wrote:
> --- On *Sat, 5/14/11, delara aghaie /<d_aghaie at yahoo.com>/* wrote:
>     From: delara aghaie <d_aghaie at yahoo.com>
>     Subject: [gmx-users] electrostatic potential
>     To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>     Date: Saturday, May 14, 2011, 1:30 PM
>     Hello all
>     I had simulated Tip4p-2005 water system with different
>     concentrations of MgCl2 and Cacl2 salts. I have calculated the
>     Surface tensions of the systems and I see that presence of the salt
>     increases the S.T of water layer.
>     Now to do more analysis I want to calculate the contributions of
>     water and ions to the electrostatic potential .
>     I should use g_potential command.
>     I need an index file. Do I need to specify water, Mg and Cl groups
>     in the index file?
>     is this command format corect?
>     g_potential -f traj.trr -n index.ndx -s topol.tpr ?

You can answer all of these questions yourself with a few seconds' worth of 
trying it out.  If there is some specific problem or unexpected result, then 
post that specifically.


>     Please let me know if I should consider anything else?
>     thanks
>     Regards
>     D.Aghaie
>     - <mailto:-emkul at vt.edu>


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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