AMBER Archive (2008)

Subject: RE: AMBER: Fully QM periodic runs

From: Ross Walker (
Date: Tue Nov 25 2008 - 10:54:24 CST

Hi Steven and Hannah

> We've recently become interested in performing periodic QM/MM calculations
> in Amber, but with a purely QM system. We certainly appreciate that there
> would be practical limitations with respect to the system size, but have
> there been any developments in Amber 10 (or planned for Amber 11) that
> would
> facilitate these kinds of calculations? Would it be feasible to make a
> small
> change to the code to get this working, or would there be significant
> barriers
> to this?

Unfortunately not. The same restriction still applies. It is not a simple
matter to do a pure QM system periodically because, as Dave mentions, one
has to include exchange terms in the periodic sum. I.e. you have to build a
periodic fock matrix in the first place. This is something I would actually
like to be able to do but I simply don't have the man power to do that and
the thousands of other things on my to do list. Sorry...

There may be some other codes out there that can do this, e.g. Gaussian does
periodic boundaries now (although probably only for ab initio calculations)
but this will likely only be for minimization. The same is true for other
codes, they are probably designed for treating infinite surfaces and crystal
lattices using the periodicity and not a biological system in condensed
phase. It wouldn't hurt to look though.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)