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

Tushar Ranjan Moharana tusharranjanmoharana at gmail.com
Fri Jul 7 11:35:01 CEST 2017

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
LJ-SR:161TYR-161TYR_com    -47.9464        1.5    10.2566    2.55572
Coul-14:161TYR-161TYR_com          0          0          0          0
LJ-14:161TYR-161TYR_com           0          0          0          0

I think it should be fine as the result didn't change much (other than the

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?

Thanks a lot for your time and effort.

"A society with free knowledge is better than a society with free food"
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB

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