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

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 14 23:18:52 CEST 2010

Jyoti Mahalik wrote:
> 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>
> 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 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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