[gmx-developers] AMBER FF validation

Berk Hess hess at kth.se
Thu Aug 23 09:27:49 CEST 2012


The current Amber force field implementations in Gromacs are based
on Eric's original ports and adapted by me with some minor changes
by Erik Lindahl to adher closer to the original Amber force fields.
The results of the Amber force fields in Gromacs have been compared
with results in Amber by Erik Thompson and Eric Sorin. I don't recall
that we explicitly checked amber99sb-ildn, but that differs only in a few
Currently nothing is being validated, as the force fields didn't change
the past years.
If new, useful force fields appear we will probably include them, but only
after validation against Amber, as we did for e.g. Charmm as well.



On 08/22/2012 11:29 PM, David Mobley wrote:
> Hi, all,
> After discussion with Eric Sorin, behind the older ffAMBER ports for 
> GROMACS, I wanted to ask a couple quick questions concerning the AMBER 
> FFs (based on ffAMBER) now distributed with GROMACS:
> 1) Are the AMBER FF distributions currently being validated against 
> the corresponding forcefields in AMBER itself? (This was done for 
> ffAMBER, on which these ports are based, but we are unclear on whether 
> anyone is currently doing this)
> 2)  Who is behind the implementation of newer AMBER forcefields in the 
> GROMACS distribution, i.e. amber99sb-ildn? Have these been validated 
> against the corresponding forcefields in AMBER?
> 3) Are there any plans for continued incorporation of and maintenance 
> of any new AMBER forcefields into the distributions?
> Eric Sorin and in discussion about validation, and may be interested 
> in validating these against the AMBER distribution if it is not 
> already being done.
> Thanks so much for your help.
> Sincerely,
> David Mobley
> Assistant Professor
> Department of Pharmaceutical Sciences
> University of California, Irvine
> -- 
> David Mobley
> dmobley at gmail.com <mailto:dmobley at gmail.com>
> 504-383-3662

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