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