# [gmx-users] potential energy between 2 energy group

Justin Lemkul jalemkul at vt.edu
Thu Mar 3 23:03:32 CET 2016

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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

>
>
>
> "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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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