[gmx-users] calculating electrostatic potential
d_aghaie at yahoo.com
Sun May 15 21:42:01 CEST 2011
--- 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
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 ?
Please let me know if I should consider anything else?
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