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 Mon Nov 21 2011 - 13:30:02 PST
