From: Chris Harrison (
Date: Wed Mar 17 2010 - 00:13:12 CDT


Please have a look at the NAMD troubleshooting guide:

Pay particularly close attention to the "Bad global exclusion count" section
and the suggested fix:

These errors generally indicate that two atoms that are (ususally
implicitly) excluded are on non-neighboring patches or are more than the
cutoff distance apart. The situation is analogous for bond, angle, dihedral,
or improper count errors.

This is often caused by similar input problems as in "Atoms moving too fast"
above. In particular, atoms with uninitialized coordinates (0,0,0) may cause
this error on the first timestep.

This will also happen if you have a periodic cell and the input coordinates
to NAMD are wrapped on a per-atom basis so that there are bonds to hydrogen
atoms extending across the cell (i.e., you load the psf and pdb in VMD and
see very long bonds to hydrogens). *You can work around this with the
ancient "splitPatch position" option, which makes every atom its own
hydrogen group (this option disables rigid bonds and hurts performance, so
don't use it normally). It's better to just fix the input coordinates so
that the bonds look normal in VMD. *

Another possibility is that some atoms are specified more than once, for
example one residue ends up in two chains. This is very difficult to spot in
VMD as these duplicate atoms have the same coordinates.


Should this fail to fix your problem, please let us know.


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                            Voice: 217-244-1733               Fax: 217-244-6078
On Sat, Mar 13, 2010 at 11:22 AM, Werner Crous <>wrote:
> Dear NAMD-users
> I setup a large system in CHARMM, done minimization and 200ps NPT dynamics,
> with no problems. However, when I tried to continue dynamics with NVT in
> NAMD I got the error listed in the subject line. I read almost every account
> of this error on the list, and it seems to me that it has to do with the way
> in which NAMD partitions the system in patches and that some of the water
> molecules in my system, that were wrapped to the unit cell by NAMD, were
> "split" in the process with some atoms of the water molecules at the top and
> others at the bottom of the unit cell. As I understand it, NAMD cannot put
> molecules with "elongated bonds " longer than the cut-off distance in a
> patch and this causes the error. I do not understand how this could have
> happened since I imaged my water molecules in CHARMM by residue. Can someone
> please tell me if there is a quick way of fixing this and how to prevent
> this error form occurring in the future?  I ran successful simulations with
> NAMD in the past and this is the first time this error occurs.
> Best regards
> --
> Werner Crous
> Scientific Computing Research Unit
> University of Cape Town
> Rondebosch 7701
> South Africa
> Phone: +27 21 650 2530 (O)
> Fax: +27 21 686 4333

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