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Running I/O intensive jobs on the cluster

1/17/2012

Software that is I/O intensive (like NWChem or any MD program) should always be forced to write in the local disk and not use NFS. If you try to do a lot of I/O over NFS, your job on the cluster will be tremendously slowed down.

Therefore, when running a job please define "scratch_dir" and "permanent_dir" to be /tmp or /scratch in the your input file.
Do not use your home directory to write!

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Force Field Parameterization with AFMM

1/8/2012

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The "Automated Frequency Matching Method" (AFMM) is a method to parameterize small organic molecules for which force field parameters are unavailable. As the title implies, we use normal mode analysis and match MM normal modes in order to reproduce the QM normal modes. The method should be ideally used for molecules that are rigid and therefore possess few minima and for parameterizing bond and angle force constants (although dihedrals can be tuned at a certain extent as well.

AFMM is currently implemented for CHARMM and AMBER force fields. Our software cannot handle the Gromacs force field because it is united-atom and therefore matching QMM and MM normal modes does not make much sense.

You can find more information about AFMM here:

Z. Cournia, J. C. Smith, and G. M. Ullmann (2005) A molecular mechanics force-field for biologically-important sterols. J. Comp. Chem., 26:1383-1399.

A. C. Vaiana, Z. Cournia, I. B. Costescu, and J. C. Smith (2005) AFMM: A molecular mechanics force-field vibrational parametrization program. Comput. Phys. Commun., 167:34-42.

Please email me at: zcournia [at] bioacademy.gr if you are interested in receiving the code, the manual and support.

Running I/O intensive jobs on the cluster

Force Field Parameterization with AFMM

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