[gmx-users] g_energy definition

[Justin Lemkul]

On 7/23/14, 11:05 PM, Andy Chao wrote:
> Dear GROMACS USERS:
>
> Thanks a lot for your supports and help!  I would like to ask more
> questions related to the output (*.xvg) of the command g_energy.
>
> 1. GROMACS computes the potential energy of an ionic liquid to be negative
> beyond a specific time.  What does negative energy of an ionic liquid
> electrolyte mean?
>

Negative energy means net attraction.

> 2. What does the calculation of the energy for "Bond," "Angle," "Proper
> Dih," "LJ-14," "Coulomb-14," "Vir-XY," "Pres-YY," etc. represent? Where can
> I find the reference that explain each term?
>

Most of the terms should be obvious.  "Bond" is the energy of bonds, "Angle" for 
angles, etc.  The "14" interactions are intramolecular 1-4 interactions.  "Vir" 
and "Pres" terms are related to virial and pressure tensors, respectively.

> 3. I would like to estimate the total free energy of an ionic liquid.  How
> should the total free energy be calculated based on the available selection?
>

You don't.  You can get an internal energy and ultimately an enthalpy from the 
.edr terms, but there is no energy term for entropy; this is true for any MD 
simulation.  There are various ways of calculating entropy in MD simulations, 
but not from the .edr file.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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