[gmx-users] Difference between gmx spol and gmx h2order in calculationg the orientation of water around surface and solute?

rose rahmani rose.rhmn93 at gmail.com
Sun Sep 9 20:07:20 CEST 2018


I study the properties of water molecules above surface which is in xy

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


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