XPLOR-NIH on Biowulf

• 3J couplings
• 1J couplings
• 13C shifts
• 1H shifts
• T1/T2
• dipolar couplings
• radius of gyration
• CSA
• conformational database torsion angle potentials
• database base-base positioning potentials for DNA
• interface to the NMR graphics package VMD-XPLOR, downloadable separately.
• embedded Python and TCL interpreters.

The advantage of running Xplor-NIH on Biowulf would be to spawn a large number of independent refinement jobs which would run on multiple Biowulf nodes. Note that each run is not parallel; the speedup is produced by the swarm of independent jobs. Thus it is ideally suited for refining multiple NMR structure models. Xplor-NIH is based on Xplor 3.851.

XPLOR was developed at Yale University, and the NIH extensions were developed by G. Marius Clore, John Kuszewski, Charles D. Schwieters, and Nico Tjandra.

XPLOR-NIH web site, including tools for use at NIH

Xplor Manual

Running Xplor-NIH on Biowulf

To submit an Xplor-NIH batch job on Biowulf, you need a PBS batch script.
Sample script, modified from Charles Schwieters.

#/bin/sh # # This is a PBS script to run parallel XPLOR-NIH jobs on Biowulf # CDS - 12/16/02 # # # PBS stuff # #PBS -N xplor-nih #PBS -S /bin/sh #PBS -m be #PBS -k oe # # cd to the 'working' directory, from where the job is being submitted. # This can also be set to an explicit pathname. # cd $PBS_O_WORKDIR # # uncomment if the script is a python script # #PY=-py # # name of XPLOR script # XPLOR_SCRIPT=test.inp # # name of output file (output will appear in script.out.#) # where # is 0-(num processors) # LOGFILE=script.out # #location of xplor # XPLOR=/usr/local/xplor-nih/bin/xplor # #list of nodes on which to run: # this to run two jobs on each node. Do not change this. # XPLOR_MACHINES=xplor_machines.$PBS_JOBCOOKIE cat $PBS_NODEFILE $PBS_NODEFILE > $XPLOR_MACHINES # # run xplor # env XPLOR_RSH="rsh -n" \ $XPLOR $PY -parallel -o $LOGFILE -machines $XPLOR_MACHINES \ < $XPLOR_SCRIPT # # clean up # rm $XPLOR_MACHINES

Submit this job with a command like:

qsub -l nodes=8 scriptname

Monitoring your job \As with all jobs on Biowulf, the individual job or the entire system can be monitored with a variety of web-based tools. On the right is an image of the monitor for all jobs belonging to one user. See the Biowulf user guide for a description of these tools. Biowulf Cluster monitors

Benchmarks