[gmx-users] g_energy questions

[Justin Lemkul]

On 7/23/14, 12:31 AM, Andy Chao wrote:
> Dear GROMACS Users:
>
> I would like to use the command g_energy to calculate the total free energy
> of an electrolyte.  I use the following command:
>

You won't get a free energy of anything from the terms in the .edr file.

> g_energy -f NPT.edr -s NPT.tpr -b 0 -e 1000 -o energy.xvg
>
>
> GROMACS4.6.5 printed out the following:
>
> Select the terms you want from the following list by selecting either (part
> of) the name or the number or a combination.  Enter your selection with an
> empty line or a zero.
>
> 1. Bond   2. angle   3. proper-Dih   4 LJ-14......
>
>
> My question is
> A. what is the definition of each selection?  Which selection should I
> choose to calculate the potential energy, kinetic energy, and the total
> energy?
>

The names are explicit.  Total, kinetic, and potential energy are labeled as such.

> B. How can I change the time axis to calculate the energy beyond 200psec?
>   What parameter must be chagned in the g_energy command?
>

The available frames are dependent solely upon how long your simulation is and 
how often you saved frames.  You can't create frames out of nothing, but if 
you're using -b and -e to parse frames, perhaps you shouldn't be, though -e 1000 
implies the .edr file contains at least 1000 ps worth of data, so stopping at 
200 ps means your simulation was only 200 ps long and -e is irrelevant.

-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

==================================================