Hi, I study the properties of water molecules above surface which is in xy plane.
I want to calculate the distribution of water polarization above surface. I didn't do polarizable simulation, i just mean the orientation of dipole moment vector if water above surface and calculate the distributios of the magnitude and y-component of these vectors. I read about some gmx analyzes but i can't decide that which are really the best for my needs. Do you think gmx spol can exactly do what i want? So what could be its difference between gmx h2order in my case? Are they really different in my case? (As both of them use dipole as water representation) What about gmx sorient? If i have an amino acid in my system too, and i wanted to calculate the orientation of water dipoles around amino acid, should i use gmx spol or gmx sorient? I know i asked many questions in one email, but they are really really important and a little confusing for me. So i really would be appreciated if you answer me. Best rehards 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.
