Jyoti Mahalik wrote:
Message: 2
Date: Thu, 14 Oct 2010 21:56:22 +0200
From: David van der Spoel <[email protected]>
Subject: Re: [gmx-users] Extracting potential energy of protein units
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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?
No. You can use the energygrps keyword in the .mdp file to decompose
short-range nonbonded interactions, but bonded interactions are not broken down
into these groups, nor are long-range electrostatics (if you used PME).
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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