Re: [AMBER] Polarizability and induced dipoles

From: Ross Walker <>
Date: Tue, 15 Jun 2010 02:31:16 -0700

Hi Thomas,

Just so I understand this properly. The chamber patch will take the
polarizability data from the charmm force field file and include it in the
prmtop file. Are the implementations of the polarizable force fields in
charmm and amber identical?

Can you just confirm that you tested things in the same way we tested things
with chamber in the first place. That is run both charmm and amber with the
charmm_dump_gold flag set and confirm that when ipol=1 in amber (and
whatever the setting is for a polarizable simulation in charmm) you get
identical answers (to machine precision) for a single point energy
calculation. Both the energies and forces should match to machine precision.

Take a look in: /amber11/AmberTools/test/chamber/dev_tests for some
examples. We need to confirm that charmm and amber (both pmemd and sander)
will give identical answers when run with polarization before we can include
this into chamber. If you can send the results directly to myself and Mark
Williamson that would be great.

Thanks for your work here.

All the best

> -----Original Message-----
> From: Mag. Thomas Taylor []
> Sent: Tuesday, June 15, 2010 1:54 AM
> To: AMBER Mailing List
> Subject: [AMBER] Polarizability and induced dipoles
> Dear AMBER users and developers,
> Please find attached two patches:
> - chamber.patch
> - dipoles.patch
> chamber.patch:
> The created prmtop file now always has a POLARIZABILITY flag. Either it
> contains
> only 0s or the polarizability data extracted from the prm file.
> dipoles.patch:
> To calculate properties from the trajectory I require the induced
> dipoles for
> each atom. According to the documentation one can define groups and
> then output
> them to the out file or something, but I feel it should be possible to
> store
> them in the trajectory file along with coordinates and velocities.
> For this purpose I have cannibalized the -mdip command line options as
> it
> appeared to be unused.
> Also introduced is the parameter ntwm in the namespace control, which
> behaves
> for dipole archiving (storing) like ntwv does for velocities.
> Please consider incorporating parts or all of the patches into AMBER11.
> Feel free to point out any bugs/problems/etc.
> HTH,
> Thomas Taylor

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Received on Tue Jun 15 2010 - 03:00:03 PDT
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