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

[Tushar Ranjan Moharana]

Hi Justin,
Thanks a lot for the valuable advice.






"A society with free knowledge is better than a society with free food"

On Fri, Jul 7, 2017 at 3:04 PM, Tushar Ranjan Moharana <
tusharranjanmoharana at gmail.com> 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?
>
> 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
>



-- 
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB