Re: namdenergy and amber trajectory

From: V.Ovchinnikov (ovchinnv_at_MIT.EDU)
Date: Tue Jul 29 2008 - 17:30:53 CDT

Are the van der Waals shifting function in Amber and cutoff the same as
the ones used in NAMD ? Although, looking at the differences,
discrepancies there would not account for such a huge effect (factor of
three?). Might want to post relevant snippets of your code.
Victor

On Tue, 2008-07-29 at 13:58 -0600, Alessandro Nascimento wrote:
> Hi everyone,
>
> I wrote a simple code to compute interaction energies between two residues.
>
> As a test, I ran a simulation in amber (sander) of a tip3 waterbox and
> i am trying now to compare the results i got with the results from
> NAMDenergy. The electrostatics interactions match pretty well. For
> vdw, however, I can't achieve a matching between my results and
> namdenergy's one. Maybe someone here can halp me to find out what I
> may be missing.
>
> Some details of the simulation:
>
> the waterbox system was prepared in leap (from amber9 suite) using
> amber ff99SB, minimized and simulated in sander with no periodic
> conditions applied.
>
> For namdenergy calculations I choose the 'debug' mode, and modified
> the namd input file to include
>
> "1-4scaling 0.83333" and "switching off", applicable for amber ff.
>
> Any ideas of what I am missing?
>
> There is a figure showing how different the results are in:
>
> http://blogdonascimento.blogspot.com/
>
> Thanks a lot,
>
> sorry for those who already got this message in amber list
>
>
> --alessandro
>

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