RE: is there any maximum limt of atom numbers in VMD or NAMD?

From: Ana Celia Araujo Vila Verde (
Date: Wed Nov 29 2006 - 10:07:10 CST


>From that error message, I'd say there is something wrong with your psf file. It seems that one of your atoms may have more than the maximum allowed number of bonds. You should specifically have a look at residues 2399 and 1 in VMD and see if there is an extra bond that shouldn't be there. Also, have a look at any log files that you may have from generating that psf, as they may point you to the origin of the error.

I hope this helps.


Ana Célia Araújo Vila Verde
Penn State University
Department of Chemical Engineering
Fenske Laboratory
University Park, PA 16802
Phone: +(1) (814) 863-2879
Fax: +(1) (814) 865-7846

-----Original Message-----
From: [] On Behalf Of youbin tu
Sent: Wednesday, November 29, 2006 12:01 AM
Subject: namd-l: is there any maximum limt of atom numbers in VMD or NAMD?

Hi all:
   When loading a membrane, which has 50318atoms. The vmd command screen gave some error and warning message such as:

    ERROR> Residue exceeded maximum number of bonds <4>
    Warning) Unusual bond between residues 2399 and 1

    Although, it looks like the molecule is very well shown in the VMD display window, but I still doubt whether the errors can bring troubles to the coming simulations using NAMD?
    In fact, my NAMD simulation really broke down when I initiate an MD simulation. So I have to trace back each step from the beginning.
    I really appreciate it if sb can give me some suggestions.


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