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

Neda Rafiee nerafiee at ipm.ir
Fri Mar 9 10:48:58 CET 2018

Dear users,
I want to calculate Phenyl dipole moment from my traj.trr file but my trajectory does not contain mass and charge. 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 the file "mcfile" to define charges of atoms:
plumed driver --mc mcfile --plumed Plumed_Inputs_7mar18/dipole.dat  --mf_trr traj_01234_pbc.trr

it does not give any error but just writing "nan" instead of giving a meaningful dipole moment.
Can you help me with this?
Thanks in advance.

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