Re: AMBER: Switching function in NAMD

From: Adrian Roitberg <>
Date: Tue, 23 Dec 2008 14:56:58 -0500

Of course it would change the results !

And that would not be the only thing in namd different than amber per-se.

Make absolutely sure that you are using the correct 1-4 scaling factors
for electrostatic and vdw. The namd defaults are wrong.


musa özboyacı wrote:
> Dear all,
> I am trying to simulate a system using NAMD with AMBER force field. I have
> just realized that, I had turned on switching function and defined a
> switching distance. Since, for AMBER does not use such switching functions,
> does this function change my results? and, should I simply give an end to my
> simulations and restart them? I am going to perform some energy calculations
> after these simulations so, does this function make my results unreliable?
> Any help is appreciated, thanks in advance!
> Musa Ozboyaci
> Koc University
> Computational Sciences and Engineering

                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry
                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society
University of Florida                         PHONE 352 392-6972
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Received on Wed Dec 24 2008 - 01:21:53 PST
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