[gmx-users] potential energy between 2 energy group

[Tushar Ranjan Moharana]

Hi Everyone,
I want to calculate potential energy between 2 coils of the same protein. I
made 2 energy groups one for each coil and use gmx energy and got the
following energy terms:

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Coul-SR:coil1-coil2    -85.7567        1.2    10.3342    5.15837  (kJ/mol)
LJ-SR:coil1-coil2      -22.9698       0.56    6.46579   -3.33975  (kJ/mol)
Coul-14:coil1-coil2              0        0.0      0.0             0.0
     (kJ/mol)
LJ-14:coil1-coil2                  0        0.0     0.0              0.0
       (kJ/mol)



*Now my doubt is can I say the addition of above energy is the net
potential energy between those 2 groups? Does this (Coul-SR) includes
hydrogen bond energy also? If not then how can I calculate it? *


*I used gmx hbond -temp 298 (298 is the temperature) after selecting groups
I got following result:*Hydrogen bond thermodynamics at T = 298 K
Fitting parameters chi^2 = 0.000649398
Q =          0
--------------------------------------------------
Type      Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward         0.022     45.795      14.000  0.000649398
Backward       -0.063    -15.875    -666.000
One-way         0.043     23.120      12.306
Integral       -0.039    -25.489    -666.000
Relaxation      0.052     19.113      11.835

*Can we calculate hydrogen bond energy from this? If not then what these
terms are.   *

Thanks for your valuable advice.



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

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