[gmx-users] Re: Extracting potential energy of protein units

[Jyoti Mahalik]

Message: 2
Date: Thu, 14 Oct 2010 21:56:22 +0200
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] Extracting potential energy of protein units
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4CB76066.8050404 at xray.bmc.uu.se>
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On 2010-10-14 21.51, Jyoti Mahalik wrote:
> Using g_energy I can extract the energy of the whole system. But I want
> to extract the energy (potential energy) of the protein units in my
> system. Is it possible to do it in GROMACS or any other application?
How would you define that?

I would like to know the potential energy of the protein units in a  
system of protein, water and salt.
  V_tot=V_prot_intra+V_prot_sol+V_prot_salt+V_sol_intra+V_salt_intra+V_sol_salt

Is it possible to get the V_prot_intra part of the total potential energy?