Problems Bionanotechnology Tutorial

From: Salvador H-V (
Date: Fri Oct 21 2011 - 22:19:01 CDT

Dear All,

I am trying to complete the Bionanotechnology tutorial. I assume that is the
most recent version, donwloaded from the tutorial pages of namd
(accompanying pdf file has a date of April 2011).

I hope that some body familiar with this tutorial can help me with the next

I have been able to follow the tutorial until I run into some problems in
section 1.4 Calibrating the force field.

In this section after some intermediate steps we have to run a simulation to
increase the temperature of a silicon_nitrite membrane.

I did the suggested steps and run the simulation:
./namd2 eq1.namd > eq1.log & (500 steps)
The simulation finished successfully.

Then, I run the second suggested simulation to equilibrate the system.
Inputs files are provided in the tutorial. So, I launched the simulation:
./namd2 eq2.namd > eq2.log &

But the simulations crashes with the following errors:
Processor 0 Exiting : Called CmiAbort
FATAL ERROR: Bad Global exclusion count!

Charm++ fatal error:
FATAL ERROR: Bad Global exclusion count!

I took a look to the dcd trajectory in vmd and the systems is well behaved,
I mean is not exploiding.
Also I tried to increase to 5000 the number steps in the simulation to
increase the temperature but without success.

Any body has found a similar problem in this particular tutorial?

Any suggestion would be greatly appreciated


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