On 8/26/12 6:01 PM, Acoot Brett wrote:
Dear Justin,
In the internet there is the following content. But if I need to measure the
non-bonded energy between residues within a protein, or between fragments
within a protein, can you advise on how to set up the energygrp?
You can use whatever custom energygrps you want, supplied with an index file.
Note that you don't necessarily need energygrp_excl to calculate interaction
energies between molecules or fragments, you just need energygrps. If you're
breaking molecules apart, it's especially difficult to use energygrp_excl
(depending on the algorithms used), and the speedup probably isn't worth it. A
rerun should only take a matter of hours, even for a rather long trajectory.
-Justin
Cheers,
Acoot
Energy group exclusions
energygrp_excl:
Pairs of energy groups for which all non-bonded interactions are excluded.
An example: if you have two energy groups Protein and SOL,
specifying
energygrp_excl = Protein Protein SOL SOL
would give
only the non-bonded interactions between the protein and the solvent. This is
especially useful for speeding up energy calculations with mdrun -rerun and for
excluding interactions within frozen groups.
----- Original Message -----
From: Justin Lemkul <jalem...@vt.edu>
To: Acoot Brett <acootbr...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@gromacs.org>
Cc:
Sent: Monday, 27 August 2012 7:09 AM
Subject: Re: [gmx-users] GROMACS command for energy calculation
On 8/26/12 5:02 PM, Acoot Brett wrote:
Dear All,
After the production MD has been done, does GROMACS has a command which can
calculate the interaction energy between any 2 residues in a frame of structure
from the MD?
Assuming you have made proper use of energygrps in the .mdp file, you can
extract nonbonded terms between these groups from the .edr file using g_energy.
If you have not set energygrps, you can create a new .tpr file and use mdrun
-rerun to recalculate the energies from an existing trajectory or snapshot.
-Justin
-- ========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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