[gmx-users] Calculating the dipole moment vectors of functional groups

[Andrew DeYoung]

Hi,

I would like to calculate the dipole moment (vector) of a functionality in
molecules, probably using g_dipoles.  For example, suppose that my molecules
have hydroxyl functionalities; I would like to calculate the dipole moment
vectors of each hydroxyl group.

I can create an .ndx file with an entry containing all of the hydroxyl group
atoms in my system.  However, if I feed this .ndx file to g_dipoles using
the -n switch, g_dipoles will of course compute the (total) dipole moment
vector of those atoms, not the dipole moment vector of _each_ hydroxyl
group.

So, I think that I will need to make individual .ndx entries for each
hydroxyl group.  Thus if I have 1000 hydroxyl groups in my system, I will
need to make 1000 .ndx entries.  I don't think so, but is there any way to
specify multiple .ndx entries in g_dipoles?  Some gromacs utilities have a
-ng switch ("Number of groups to consider"), but it does not seem that
g_dipoles has this.  Do you think that the best way would be for me to write
a bash script to call g_dipoles 1000 times with the 1000 .ndx entries?

Thanks for your time!

Andrew DeYoung
Carnegie Mellow University