running NAMD on beowulf cluster

From: Nitin Bhardwaj (
Date: Wed Apr 05 2006 - 14:17:31 CDT

Dear NAMD users,
  I am having trouble running NAMD on a beowulf cluster. I am using
this batch file to run NAMD (this is a modified version of the batch
file i found on the web).

#PBS -k oe
#PBS -m be
set path=(/home/homes53/nbhard2/C2/wrong/namd2 $path .)

charmrun /home/homes53/nbhard2/C2/wrong/namd2 +p$np ++nodelist
~/namd.$PBS_JOBID wrong_y_90.conf >& test.out

I run it by saying:

qsub -v np=8 -l nodes=4:smp wrong_y_90.in2

or run this batch file (worng_y_90.in2) file with any 4 nodes having
dual processor.

The error it gives is:

ERROR> No such nodelist file

Please let me know where I am going wrong. I also do not understand
the function of the command 'make-namd-nodelist' in my batch file.

Any help would be greatly appreciated.

thanks a lot in advance.

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