[gmx-users] frame with lowest energy

[Alexander Alexander]

Hello there,

Concerning to the issue raised by Sana and "gmx cluster", what would be the
potential known useful geometric criterion of amino acids in each of below
systems:

1) A single amino acid in aqueous solution?

2) A single amino acid adsorbed on a solid surface in aqueous solution?

Thanks.
Regards,
Alex

On Thu, Jun 9, 2016 at 1:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

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