[gmx-users] protein protein interaction: side chain contribution

[Justin Lemkul]

On 7/7/17 5:34 AM, Tushar Ranjan Moharana wrote:
> Hi Justin,
> Thanks a lot for the advice. It looks like I had put one atom in the wrong
> index group. After correction my results looks as follows:
> 
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> ------------------------------------------------------------
> -------------------
> Coul-SR:161TYR-161TYR_com   -75.0549        1.7    17.8261    8.26634
> (kJ/mol)
> LJ-SR:161TYR-161TYR_com    -47.9464        1.5    10.2566    2.55572
> (kJ/mol)
> Coul-14:161TYR-161TYR_com          0          0          0          0
> (kJ/mol)
> LJ-14:161TYR-161TYR_com           0          0          0          0
> (kJ/mol)
> 
> I think it should be fine as the result didn't change much (other than the
> LJ-14).
> 
> As per your suggestion, calculation of kinetic energy by gmx traj or
> energy(after saving only desired atoms in the trajectory) are not
> meaningful. Is there any way to compute it?
> 

You can get it from gmx traj if you correctly account for constraints (see 
previous mailing list posts on this), but again I maintain it's very unlikely to 
be scientifically useful.  A larger side chain will have a larger KE because 
there are more atoms over which you are summing 0.5*mv^2.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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