[gmx-users] How to calculate protein-surface interaction energy

[Justin Lemkul]

On 10/16/14 5:46 AM, James Lord wrote:
> Dear users,
> I want to calculate the interaction energy (energy versus time) of a
> protein (Lysozyme) adsorption process (20ns) on to a solid surface
> (polyethylene).
> when I use gmx energy -f md.edr -o energy.xvg and then selecting total
> energy I end up with a messy graph!!! I am doing some wrong? secondly, Is
> there any way to average the energy over the last 10ns of MD trajectory in
> Gromacs??

Total energy is just as it says, the total energy of the system.  If you want to 
measure interaction energies, you need to make use of energygrps in the .mdp 
file to decompose (short-range) nonbonded energies.  Note that the mesh term 
from PME is not decomposable in any straightforward way.  If you did not use 
energygrps in the .mdp file for the run, create a new .tpr file and recalculate 
the energies in the existing trajectory with mdrun -rerun.

-Justin

-- 
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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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