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. NEDA -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
