AMBER Archive (2008)

Subject: Re: AMBER: Switching function in NAMD

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Tue Dec 23 2008 - 13:56:58 CST

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.

Adrian

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
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu