[gmx-users] frame with lowest energy

[Justin Lemkul]

On 6/8/16 8:37 PM, Sana Saeed wrote:
> hello gromacs users and experts,
> i have performed 10ns complex simulation of Protein and ligand-complex, now i need the best conformation for further analysis (alchemical analysis: binding free energy simulations). i want to choose best initial structure for further study. how would i know which frame has lowest energy? i studied gmx energy tool but couldn't find way.

Cluster the trajectory based on some known useful geometric criterion.  The 
lowest energy state should be the most populated one.  Note that energies that 
come out of simulations are not free energies (at least, not without significant 
post-processing and analysis) so you can't use e.g. quantities from gmx energy 
to get an answer.  10 ns isn't likely long enough to really get anything 
definitive, though.

-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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