From: Rachel (
Date: Wed Jul 25 2007 - 11:11:34 CDT

Dear all,

I have VMD installed on IBM cluster, and I need to run some scripts with VMD
which takes long time to finish when ran interactively, therefore I am
wondering if I submit to queueing system it may be much faster, here is the
script I used to submit the job:


#@ shell = /bin/bash
  #@ job_name = model_VMD

  #@ job_type = parallel
  #@ cpus = 16
  #@ node_usage = not_shared
  #@ bulkxfer = yes
  #@ wall_clock_limit = 06:00:00
  #@ account_no = a129
  #@ output = $(job_name).$(schedd_host).$(jobid).out
  #@ error = $(job_name).$(schedd_host).$(jobid).err
  #@ notification = never
  #@ queue

  # suggested environment settings:
  export MP_EAGER_LIMIT=65536
  export MP_SHARED_MEMORY=yes

   vmd mol new model.prmtop

   vmd mol addfile model_md1to5.mdcrd type crdbox waitfor all

   vmd source myscript.tcl

   vmd myscript

And the following are the output and error messages:

Info) VMD for AIX5_64, version 1.8.6 (April 6, 2007)
Info) Email questions and bug reports to
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1 , 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 16 CPUs detected.
Info) Free system memory: 0MB (-9223372036854775808%)
Info) VMD for AIX5_64, version 1.8.6 (April 6, 2007)
Info) Exiting normally.

/var/loadl/execute/l1f402.211658.0/run_VMD: mol: command not found
/var/loadl/execute/l1f402.211658.0/run_VMD: mol: command not found
/var/loadl/execute/l1f402.211658.0/run_VMD: proc: command not found
/var/loadl/execute/l1f402.211658.0/run_VMD: puts: command not found
/var/loadl/execute/l1f402.211658.0/run_VMD: myscript.tcl: line 7: syntax
error near unexpected token `i'

I haven't used VMD in this way before, therefore not sure whether it is the
right way to do so. What I really need is a way to use VMD for analysis that
takes long time that I can logoff without killing the process.

Thank you in advance for any advice.

Kind regards,