[gmx-users] Water properties above surface

rose rahmani rose.rhmn93 at gmail.com
Sun Sep 2 18:52:26 CEST 2018


I study the interaction of different amino acid above surface in presence
of (TIP3P)water in physiological ion concentration(150mM) and i calculated
PMF for different distances of AA above surface.
Now, i want to find different proofs which prove the importance of water
molecules, amino acids different polarities and hydrophobicities and water
layer formed above surface in the quality of AA interaction with surface.
I searched about every tools in lovely GROMACS to calculate these
properties; So,

1- We all know about different amino acids properties(polarity,
hydrophobicity, ...) generally, but i could not find any tool in GROMACS to
quantitively prove these properties (amino acids) in different systems.
However i think it is not possible at all;) , we should search about
different clues,... . for example i want to show the distribution of water
in RADIAL distances around AA  to show the hydrophobicity/phility but i
don't know which tool can do it? is gmx spol appropeiate for these goals?
( I will refer you to these question's attached filehttps://

2- number density profile of water above surface which causes forming
solvent layers... fortunately i could do it by gmx density. but how about
the orientation of water molecules near the surface? how can i show that?
can gmx hydorder or gmx sorient does?
3- and what i have never understand about gmx SASA is that; for example
when i choose protein and SOL group, what does it exactly calculate? does
it will calculate the solvent area around AA??

sorry for multiple question
I would be grateful if you answer to them.

Best regards


More information about the gromacs.org_gmx-users mailing list