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

[James Lord]

Hi Justin,
Thanks, the .mdp is the same as your tutorial for lysozyme, Can you explain
a bit more what to do? if I want to have total energy= vdw and
electrostatic?
Cheers
James



On Fri, Oct 17, 2014 at 12:51 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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