On 4/13/18 2:42 AM, rose rahmani wrote:

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

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

jalem...@vt.edu | (540) 231-3129


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