[gmx-users] calculating pairwise interactions

Justin Lemkul jalemkul at vt.edu
Sun Apr 15 16:43:49 CEST 2018

On 4/15/18 7:23 AM, Mark Abraham wrote:
> Hi,
> You can use energy groups in a tpr for a rerun, but you will not get any
> long-range contribution. Neither does any force field that I know of
> produce a useful quantity from such a calculation.

Again, I'll bang the drum a little bit for CHARMM here - we do 
explicitly target QM interaction energies with (at least) water, 
therefore providing a standard of reference for all interaction 
energies. There are other cases in which we balance against additional 
interactions on the QM level. It's the only force field I know of that 
explicitly does this (most others either compute charges in a continuum 
model or just go straight for DGsolv).

Decomposing LJ vs. Coulomb within the short-range nonbonded interaction 
energy is still totally useless, but I would argue that the total 
interaction energy can be meaningful, at least with CHARMM.


> Mark
> On Sun, Apr 15, 2018, 06:46 Sahithya S Iyer <sah2714 at gmail.com> wrote:
>> Hi gmx users,
>> Can anyone please tell me how to get the values for pairwise interactions
>> from a gromacs trajectory. I would like to get the pairwise energy
>> interaction values (van der waal and electrostatics) for each pair.
>> Thanks in advance,
>> Sahithya.
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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