AMBER Archive (2009)

Subject: Re: [AMBER] Any link to a major QM code?

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Sun Feb 15 2009 - 20:59:01 CST

To expand on Gustavo's answer.

Amber has been interfaced with Pupil, a 'broker' program.
So far it talks to gaussian and siesta on one side, and amber (and
dlpoly) on the other side.

See:
“A versatile AMBER-Gaussian QM/MM interface through PUPIL.” Juan Torras,
Gustavo de M. Seabra, Erik Deumens, S.B. Trickey and Adrian E. Roitberg.
Journal of Computational Chemistry. 29:10, 1564-1573 (2008)

for the general ideas, and:

"A Multiscale Treatment of Angeli’s Salt Decomposition"
Juan Torras, Gustavo de M. Seabra and Adrian E. Roitberg
J. Chem. Theory Comput., 2009, 5 (1), pp 37–46

For a particular application.

We are working on adding the following implementations at this time:

gamess
nwchem
Q-chem

The API for Pupil should allow almost anyone to add whatever program you
desire. In fact, we would love some help with a couple of the
implementations.

Cheers
Adrian

Gustavo Seabra wrote:
> On Sun, Feb 15, 2009 at 12:58 PM, Francesco Pietra wrote:
>> I came across an internet unofficial announcement of charmm software
>> having been linked to gamess-us software for executing md-mm. If true,
>> i guess it was a move from the charmm side as gamess-us is free
>> software (which i am installing for resp charges).
>
> What do you mean by md-mm? If what you are looking for is just being
> able to do QM/MM MD, where the QM part is calculated by an external QM
> program, we've had this in Amber for a while now, through the PUPIL
> interface.
>
>> Question: is any similar plan from the amber side? I suspect that dftb
>> will not be enough, as far as md-mm is concerned, although all that
>> glitters may not always be gold.
>
> I don't really understand what you mean about DFTB here... It is not
> an interface with an external program: The DFTB implementation is all
> inside Amber, just as any other QM method available there.
>
> Gustavo.
>
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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry

                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu

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