On 3/3/16 2:12 AM, Tushar Ranjan Moharana wrote:
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
It's the short-range interaction energy. That may or may not reflect something
that has any physical meaning.
hydrogen bond energy also? If not then how can I calculate it? *
Hydrogen bonds are primarily electrostatic in nature. There's no discrete
energy term for it, but it's included in what you've calculated.
*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. *
I suggest you read the reference to the method you're trying to use before
using it.
-Justin
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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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