Re: namdenergy and amber trajectory

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jul 30 2008 - 00:46:57 CDT

Hi Alessandro,
could you send me (off-list) all the namd-temp* files generated from
running with debug on (but please make the dcd as small as possible), as
well as the amber input file you used? I'm a total amber n00b but can at
least try to sanity check the files namdenergy is using.
Best,
Peter

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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