[gmx-users] Polarizability analysis

Justin Lemkul jalemkul at vt.edu
Sun Apr 15 16:46:06 CEST 2018

On 4/13/18 2:42 AM, rose rahmani wrote:
> Hi
> I did umbrella sampling and calculate PMF for different aminoacid in
> different distance from surface. Now i want to discuss about the results.
> First i used gmx sasa to prove that for example amino acid(tyrosine) with
> more surface (it's aromatic) had more binding energy in comparison to
> another...
> But sometimes its hard to compare different AA, so i want to calculate AA's
> polarizability. Is there any analysis in gromacs to calculate that?
> If yes, is it probable that i get wrong results because some aminoacids are
> not too different in size and polarizability? And are in SOL, so may affect
> all these properties?
> Do you have better idea?

If your simulation wasn't polarizable, there's no way to extract such 



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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