RE: AMBER: ptraj dipole calculation in QMMM simulation

From: Ross Walker <>
Date: Fri, 9 Feb 2007 10:53:30 -0800

Dear Evan,
This is a tough one. It never occurred to me that someone might want to
calculated the dipole moment as a function of time from the QM region. At
the moment this information is not calculated. One would need to modify the
code to do this. Ideally you want the true QM dipole moment in the solvent
field from the electron density. You can approximate this by having the code
write the Mulliken charges during the QM calculation and then manually
calculate the Mulliken charge dipole moment from the mdout file using a
suitable script.
In terms of ptraj what you are getting is the dipole moment due to whatever
resp charges you have in the prmtop file for the QM atoms. These are ignored
in the actually QM/MM MD calculation and so you can't really use ptraj to
calculate the QM dipole moment.
So, short answer is that this functionality is missing at present, sorry.
I'll add it to my list of additions for the next version of Amber.
All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
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From: [] On Behalf Of
Evan Kelly
Sent: Friday, February 09, 2007 10:37
Subject: AMBER: ptraj dipole calculation in QMMM simulation

Hi everyone,

I am studying a QMMM system (quantum solute molecule in a box of TIP3P
water) and was hoping to gain some electrostatic information about the
solute. I can use ptraj to calculate the dipole moment of the solute, but
can anyone tell HOW this is calculated? i.e. are the Mulliken charges used
in a point charge dipole calculation? Does anyone know what units the dipole
moment is outputted in?


Evan Kelly

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Received on Sun Feb 11 2007 - 06:07:36 PST
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