Re: mass of atoms changable?

From: Jim Phillips (
Date: Wed Aug 30 2006 - 19:52:50 CDT

You could modify the part of the code that tries to tell if an atom is a
hydrogen. There are three places in Molecule.C that look like this:

     if (atoms[i].mass <=3.5) {
       atoms[i].status |= HydrogenAtom;
     } else if ((atomNames[i].atomname[0] == 'O') &&
          (atoms[i].mass >= 14.0) &&
          (atoms[i].mass <= 18.0)) {
       atoms[i].status |= OxygenAtom;

It's easy to find, just search for HydrogenAtom. Change the mass limit
for hydrogen and that should do it.


On Wed, 30 Aug 2006, E. Prabhu Raman wrote:

> I am trying to use NAMD to simulate a Coarse Grained model of protein(a polymer, which is an unbranched chain of beads).Thus,I have only C-alphas in my model.
> I have prepared X-plor format parameter file and a .psf file. When I start my simulation in NAMD using these files, it stops and complains about having H-H bonds present.I found out that it is because I set the mass of C-alphas in my .psf file to 1.00. When I change it to 12.00, NAMD runs fine.
> My question:
> Is there any way in which I can set a mass of 1.00 for my C-alphas?
> Thanks
> Prabhu
> E.Prabhu Raman
> Ph.D Student,Bioinformatics & Computational Biology
> George Mason University

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