[gmx-users] Polarizability analysis

[Justin Lemkul]

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 
information.

-Justin

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

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jalemkul at vt.edu | (540) 231-3129
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