[gmx-users] calculating pairwise interactions
jalemkul at vt.edu
Sun Apr 15 16:43:49 CEST 2018
On 4/15/18 7:23 AM, Mark Abraham wrote:
> 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.
> 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,
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
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