[gmx-users] Calculating the dipole moment vectors of functional groups
adeyoung at andrew.cmu.edu
Fri Nov 9 16:09:06 CET 2012
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
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!
Carnegie Mellow University
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