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Hostname: quantum2.mit.edu
Quantum2 is a 20-node cluster installed in October 2007, which features high-memory nodes for quantum-chemical calculations.

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Status notes

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Nodes 4 and 14 (n004 and n014) are currently inaccessible, due to apparent hard disk problems.

Node information

The table below lists the memory and swap file size of each node on Quantum2, along with the amount of space used and free in each node's local /scratch/ directory. This information is current as of April 1, 2010.

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Available Software

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Software Available:A number of software packages have been installed in /home/gpw501/software/
Please contact gwood@mit.edu for any questions, a very limited usage guide is given below

GAMESS-US quantum chemistry package.

    Usage:  /home/gpw501/software/gamess/rungms JOB VERNO NCPUS >& JOB.log

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            JOB is the name of JOB.inp file to be executed
            VERNO is the current version of gamess (01 at the time of writing)
            NCPUS number of cpus   
      you must make a scratch directory that matches your user name on the
      node you are running from i.e. /scratch/$USER

See GAMESS homepage for more details. executed
VERNO is the current version of gamess (01 at the time of writing)
NCPUS number of cpus
you must make a scratch directory that matches your user name on the
node you are running from i.e. /scratch/$USER see: http://www.msg.ameslab.gov/GAMESS/^{Image Removed} for more details

CPMD (QMMM version) plane-wave/PP quantum CP and BO dynamics.

    Usage:  mpirun -n NCPUS cpmd.x JOB PATH-TO-PPs >& JOB.out

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            mpirun should be set to /opt/openmpi/tcp-gnu/bin/mpirun in your .bashrc

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            NCPUS number of cpus
            JOB name of job file to be executed 
            PATH-TO-PPs the path to a pseudo potential library (see for eg /home/gpw501/software/cpmd/pseudos/

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            JOB.out name of output file

See CPMD see: http://www.cpmd.org/^{Image Removed} for more details.

Amber10 amber Amber 10 molecular dynamics program.
executables Executables are located in /home/gpw501/software/amber10/exe/
see http://ambermd.org/^{Image Removed} for more details

Gromacs molecular dynamics program.
Installed Was installed as root so binaries for MD and the gromacs tools are located in /usr/local/bin/
see website for details: http://www.gromacs.org/^{Image Removed}

propka electrostatic and pka computations for proteins.
Usage: see See /home/gpw501/software/propka2.0src/README_PROPKA2.0

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Status notes

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Nodes 4 and 14 (n004 and n014) are currently inaccessible, due to apparent hard disk problems.

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Node information

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The table below lists the memory and swap file size of each node on Quantum2, along with the amount of space used and free in each node's local /scratch/ directory. This information is current as of April 1, 2010.