Hi, 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:// www.researchgate.net/post/How_can_i_calculate_the_distribution_of_water_polarization_above_surface ) 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 Rose -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.