Re: dummy atom mass changed

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Mon May 04 2009 - 15:33:57 CDT

Ly,

With 0 charge, 0 mass, and 0 radius the dummy particle is effectively the
same as no atom .... which is of course the desired effect usually.
Assuming you're not doing something unusual, then you don't need the dummy
particle. You should be able to just make the Na disappear.

The FEP tutorial may be of help in setting up calculations. This tutorial
is for NAMD 2.6 but the system setup process should be the same as
NAMD2.7b1.

NAMD2.6 FEP tutorial:
http://www.ks.uiuc.edu/Research/namd/tutorial/fep/AlchemicalFEP-Mar2008.pdf

Required files for tutorial:
http://www.ks.uiuc.edu/Research/namd/tutorial/fep/AlchemicalFEP-Mar2008.zip

C. 

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Mon, May 4, 2009 at 2:54 PM, yun luo <luoyun724_at_gmail.com> wrote:
> Hi,
>
> I'm using NAMD2.7 for running FEP. I need to disappear a sodium ion in my
> membrane. So I overlay a dummy atom with 0 mass 0 charge 0 radius on a
> sodium ion. But I got a warning below:
>
> Warning: FOUND 1 ATOMS WITH ZERO OR NEGATIVE MASSES!  CHANGED TO 0.001
>
> I'm wondering if the nonzero mass will effect the energy? If yes, how to
> stop this automatic changing?
>
> Thanks!
>
> Ly
>

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