[MMTK] Adding/modifying forcefields

konrad.hinsen at laposte.net konrad.hinsen at laposte.net
Tue Jan 4 20:39:42 CET 2005

On 04.01.2005, at 14:22, david.evans at ulsop.ac.uk wrote:

> I started on implementing Amber99, and remembered something I should
> have mentioned before, which is that Amber99 uses exactly the same
> charges and atom types as Amber94 (in fact in the main Amber program
> they use the same .lib files). So the implementation is  simple (I

So what is different then? I thought that at least the charges had been  
revised with newer quantum chemical calculations.

> However, in testing I've not been able to get the Amber94 ff in MMTK
> to give the same energies as the main Amber 8 program (sander), for a
> DNA duplex in a infinite universe with no cutoffs. Similarly for my

I didn't do many tests for the simple reason that I don't have Amber.  
But for about five example files that a colleague prepared for me  
together with Amber evaluations (that must have been Amber 5 or 6 at  
the time), I got the same energies and forces up to six or seven  
digits, which is pretty good for different implementations.

The first thing to check in case of a discrepancy is which term causes  
it. In MMTK, do

	print universe.energyTerms()

I suppose there is something similar in Amber.

Konrad Hinsen
Laboratoire Leon Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: hinsen at llb.saclay.cea.fr

More information about the mmtk mailing list