Low global exclusion count

From: matziast_at_med.uth.gr
Date: Tue Nov 08 2011 - 04:23:47 CST

Hi,
I encountered a problem while I was trying to run a minimization wih 50 steps
and an equilibration with 200000 steps with the same script. The simulation
contains also a file with fixed atoms. The message is the following:

REINITIALIZING VELOCITIES AT STEP 50 TO 300 KELVIN.
TCL: Running for 200000 steps
FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or
cutoff too small

I read at user guide of namd that it is likely to exist something wrong with the
input coordinates, such as the atoms with uninitialized coordinates or different
atom orders in the PDB and PSF file. The second does not happen. The first I did
not understand.
I would appreciate if anyone can help me.
Thank you in advance.

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