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TINKER on Biowulf and Helix
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TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special featuresf for biopolymers. It is designed to be an easily used and flexible system of progrms and routines for molecular mechanics and dynamics as well as other energy-based and structural manipulation calculations. TINKER provides a set of relatively small programs that interoperate to perform complex computations. New programs can be easily added by modelers with only limited programming experience.

Citation

If you make significant use of the package, please complete and return by regular post the license form available with the full distribution and via a link below. These forms are used to aid in convincing colleagues that TINKER is used outside of Washington University. They help us justify further development of the programs. We try to respond to email as time allows. Comments and questions are always welcome and should be directed to Jay Ponder at ponder@dasher.wsutl.edu.

On Helix

To use TINKER on either system, you must load the module.

module load tinker
newton molecule -k test a a 0.01

You can replace newton with any of the other TINKER progam names listed below.

bar       document  minimize  monte     optirot  poledit    
pssrigid  sniffer   testgrad  timer     vibrate  xyzint
alchemy   correlate dynamic   minirot   newton   optrigid  
potential pssrot    spacefill testhess  timerot  vibrot   
xyzpdb    analyze   crystal   gda       minrigid newtrot   
path      prmedit   radial    spectrum  testpair torsfit  
xtalfit   xyzsybyl  anneal    diffuse   intedit  nucleic   
pdbxyz    protein   saddle    superpose testpol  valence  
xtalmin   archive   distgeom  intxyz    molxyz   optimize  
polarize  pss       scan      sybylxyz  testrot  vibbig   
xyzedit

For TINKER help, please read the TINKER User's guide for more, detailed information.

Running a Single Batch Job on Biowulf

Create a batch input file, run_Tinker:

#/bin/bash
# ----- this file is run_TINKER -----

module load tinnker
cd /data/$USER
newton molecule -k test a a 0.01

The job can be submitted with

sbatch run_TINKER

This command will submit the job to 2 cores and 4GB of memory. If you need more memory than the default 4 GB, use

sbatch --mem=#g run_TINKER
Running a swarm of MToolbox jobs on Biowulf

The swarm program is designed to submit a group of commands to the Biowulf cluster. Each command is represented by a single line in the swarm command file that you create, and runs as a separate batch job. See the swarm page for more information.

Create a swarm command file, TINKER_swarm. Example:

cd /data/$USER/tinker1; newton molecule -k test a a 0.01
cd /data/$USER/tinker2; newton molecule -k test2 a a 0.01
cd /data/$USER/tinker3; newton molecule -k test3 a a 0.01
cd /data/$USER/tinker4; newton molecule -k test4 a a 0.01

Submit this to the batch system with the command:

swarm -f TINKER_swarm --module tinker

If each TINKER job requires more than the default 4 GB of memory, use

swarm -g # -f TINKER_swarm --module tinnker

For information on how to monitor your job(s),see Monitoring Jobs.

Running TINKER interactively

If you want to run your job interactively, you can allocate a node for interactive use. Once the node is allocated, you can type commands directly on the command-line. Example:

[user@biowulf ~]$ sinteractive
salloc.exe: Pending job allocation 15323416salloc.exe: job 15323416 queued and waiting for resourcessalloc.exe: job 15323416 has been allocated resourcessalloc.exe: Granted job allocation 15323416salloc.exe: Waiting for resource configurationsalloc.exe: Nodes cn1640 are ready for job
[user@cn1640 ~]$ cd /data/$USER/tinker
[user@cn1640 dir]$ newton molecule -k test a a 0.01

If you need more memory than the default 4 GB, use sinteractive --mem=#g

Documentation

You may direct questions about the building or use of the TINKER package to tinker@dasher.wustl.edu. TINKER related questions or comments of more general interest can be sent to the Computational Chemistry List, http://www.ccl.net.