[gmx-users] g_dipoles and index files

[ali.hassanali.1]

Hello,

I just started using gromacs 2 weeks ago and I am trying to simulate a
small polymer made up of three residues : Lys-Trp-Lys in water. I was
trying to study the dipole moment of the Trp as well as determine its
autocorrelation function and g_dipoles does that for us I believe. I was
however not sure how to use the index file with that. I read several posts
saying that this function uses "molecule numbers" as the index. If I am
using Trp to determine its dipole, do I just use its residue number in the
index file? I tried doing that and my values are way off from empirical
results. Trp has a residue number of 2 in my simulation but it gives me a
dipole moment of about 2.25. Any suggestions/ideas will be appreciated.

Ali Hassanali