[gmx-users] minimization for final configuration

[Dr. Vitaly Chaban]

Indeed, it is unlikely that averaged coordinates of certain structure
versus time correspond to something physically meaningful.

How do you average them, by the way? And what for, please?


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Tue, Sep 30, 2014 at 12:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 9/30/14 3:36 AM, Mahboobeh Eslami wrote:
>>
>> hi GMX users
>> i have simulated the protein-ligand complex by gromacs for 20ns.
>> The average for the final structure of 18 to 20 nanoseconds has been
>> achieved.is minimization for the final average structure required?Sincerely.
>>
>
> An average structure might be totally unphysical.  Energy minimization of an
> unphysical structure leads you to something that is probably useless.  I'd
> suggest doing clustering if you're interested in the predominant
> conformation(s) during a certain time period of the simulation.
>
> -Justin
>
> --
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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