VMD-L Mailing List

From: mpincu (mpincu_at_uci.edu)
Date: Fri Jan 11 2013 - 15:28:51 CST

Hello,

I have a trajectory (*.xyz) file, with an additional field after the
coordinates that contains the Mulliken charge of the atom. My system is
a charged molecule (gas phase simulation). I was wondering if there is
any tool to create a representation of the dynamic charge distribution
along the trajectory ?
I did look briefly at PME electrostatics extension, but I don't really
understand what kind of input it expects; clearly it does not understand
to read the charge from the xyz file.
Can anyone suggest a workaround ? For example, can I transform my
input file or perhaps I should create a charge input file ? What type of
inputs does PME Electrostatics expect.
Thanks,

Madeleine