[gmx-users] dipole moment for one residue of the whole protein

Justin Lemkul jalemkul at vt.edu
Fri Mar 9 14:57:43 CET 2018

On 3/9/18 4:43 AM, Neda Rafiee wrote:
> Dear users,
> I want to calculate Phenyl dipole moment from my traj.trr file but my trajectory does not contain mass and charge.

Trajectories never have mass and charge; those are fixed aspects of a 
system and are therefore in the topology (.tpr file).

> I used "gmx dipole " command for this purpose but it gives me error that Phenyl is not a whole molecule (actually because it is part of my protein which is a  molecule in its own). I also used Plumed and wrote mass and charges in

What you need to consider will depend on the force field convention. A 
dipole moment is only meaningful for a group with integral charge. A 
phenyl ring itself is unlikely to satisfy that requirement, but probably 
the entire side chain (including the CB methylene group) will.

You haven't actually shown us what you tried to do (command line, index 
group, etc) so it's hard to say what the actual solution might be, but 
it should certainly be possible to compute a dipole moment of a side 
chain. Don't expect it to show you anything useful, though. It will 
probably just be a constant number, or very close to it, as additive 
force fields don't change their electronic structure, and the only 
changes in dipole moment will come from bond stretching.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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