Hi there,
For amber in gromacs you can use acpype. Results from their testing are
here:
http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx
Oliver
On Mon, Nov 21, 2011 at 8:58 PM, George M Giambasu <giambasu.gmail.com>wrote:
> For using amber ff's in namd check this:
>
> http://ambermd.org/namd/namd_amber.html
>
> To get the right electrostatic energies you have to modify the COULOMB
> constant in namd to match the one used in sander/pmemd. I used an RNA
> system for comparison, but, as a further check, you can take alanine
> dipeptide and compare the energies that you get from both programs.
>
>
> George
>
>
> On 11/21/2011 03:00 PM, Thomas Evangelidis wrote:
> > Dear AMBER users,
> >
> > Is anyone aware of any benchmark analysis about the implementation of the
> > amber99sb force field (or any of its variants: 99sb-ildn, 99sb-nmr) in
> > AMBER and in GROMACS or NAMD? I am interested to know in what extend the
> > energies correlate and if the results agree with experimental data.
> > Differences in speed would be also interesting but of secondary
> importance.
> >
> > thanks in advance.
> > Thomas
> >
> >
> >
>
>
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Received on Tue Nov 22 2011 - 02:30:03 PST
