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

[Tushar Ranjan Moharana]

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?

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