[gmx-users] Polarizability analysis

rose rahmani rose.rhmn93 at gmail.com
Fri Apr 13 08:43:10 CEST 2018


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?

Thank you so much

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