[gmx-users] PROTEIN-LIGAND SIMULATION

[Justin Lemkul]

On 2/17/17 8:43 AM, Subashini .K wrote:
> Hi gromacs users,
>
>
> In order to calculate binding energy of single protein inhibitor complex through simulations, how long should we run the calculations?
>
>
> Is 2ns sufficient?
>

The answer to this question is always: "have the observables of interest converged?"

>
> How to obtain results and plot time (in ps) along x-axis and binding energy (kJ/mol)along y-axis?
>

If you're looking for a binding free energy, you can try an MM/PBSA 
post-processing calculation, but the standard for doing this is a series of free 
energy calculations (either alchemical perturbation or a PMF).  A single, 2-ns 
MD run of a protein-ligand complex is unlikely to yield any sort of reliable 
result.  I doubt the system is even fully relaxed over such a short time period.

-Justin

>
> Had completed two equilibration phases (NVT and NPT)and then used the command for production MD (for 2ns).
>
>
> Can someone help?
>
>
> Thanks,
>
> Subashini.K
>

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

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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