From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Mon May 04 2009 - 15:33:57 CDT
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
NAMD2.6 FEP tutorial:
Required files for tutorial:
-- 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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