RE: AMBER: &dipoles output in QM/MM simulations

From: Ross Walker <>
Date: Thu, 1 Nov 2007 10:12:52 -0700

Hi Seongeun,

Amber 9 doesn't currently support the calculating of dipoles for QM atoms.
To do this "correctly" would be difficult. However doing it with mulliken
charges is not very difficult although of course you have to accept the
approximations that this involves. From your email it seems that you would
be happy with QM dipoles calculated using mulliken charges so please try
applying the attached patch to your amber9 tree. Note this assumes your
amber9 tree is fully patched already with the latest bug fixes.

Save file in $AMBERHOME/src/sander/

cd $AMBERHOME/src/sander/
make clean
patch -p0 <qmmm_mchg_dipoles.patch
make sander
mv sander ../../exe

NOTE: This is something I hacked together in a few minutes. I do NOT have
time at the moment to test it - other than to check it compiles...

So "caveat emptor". You will need to test this yourself thoroughly to make
sure it gives the correct answer. I would suggest setting up a small pure
QM system in gas phase, say methane. Then run a few steps saving the
coordinates on every step and printing the mulliken charges. This way you
can calculate what the answer should be manually yourself and compare it to
what the code gives. Then try again with QM/MM - say two methanes side by
side, one QM one MM and again check what the code gives to what your manual
calculations give.

Note 2: I have absolutely no idea what will happen to the printed dipoles
if you are using link atoms!

or if it will work in parallel. It probably will but I didn't try it...

Good luck,


|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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> -----Original Message-----
> From:
> [] On Behalf Of Seongeun Yang
> Sent: Thursday, November 01, 2007 03:44
> To:
> Subject: AMBER: &dipoles output in QM/MM simulations
> Hi all,
> I'd like to get dipole moments in QM/MM calculations, using
> coordinates and Mulliken charges.
> But the &dipoles option doesn't seem to do that.
> Because the mdcrd file size would be too large to save as
> frequently as every few femtoseconds,
> it's desirable to calculate dipole moments during md
> simulations, not by postprocessings.
> Do I have to modify the relevant codes to do this?
> If there is some other nice way to do this during
> simulations, please let me know.
> Thanks.
> Seongeun
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Received on Sun Nov 04 2007 - 06:07:28 PST
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