namdenergy and amber trajectory

From: Alessandro Nascimento (
Date: Tue Jul 29 2008 - 14:58:56 CDT

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:

Thanks a lot,

sorry for those who already got this message in amber list


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