[gmx-users] Protein-ligand

[RAHUL SURESH]

Dear Justin,
Thank you

But What do you mean my appropriate energygrps.? Protein ligand.? Will that
give interaction energy between ligand and protein.?
On Wed, 19 Apr 2017 at 5:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/19/17 6:50 AM, RAHUL SURESH wrote:
> > Dear Gromacs users
> >
> > how to determine the interaction energy between ligand and protein at
> each
> > frame of simulation?
> >
>
> Set appropriate energygrps in the .mdp file, create a new .tpr and use
> mdrun
> -rerun to recalculate the interaction energies from the existing
> trajectory.
> This quantity may or may not be physically meaningful, depending on the
> details
> of the force field.
>
> -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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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*