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Manuscript Title: g-permute: Permutation-reduced Phase Space Density Compaction
Authors: F. Reinhard, O.F. Lange, J.S. Hub, J. Haas, H. Grubmüller
Program title: g-permute
Catalogue identifier: AECJ_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 180(2009)455
Programming language: C.
Computer: PC-compatible running Linux.
Operating system: Linux.
RAM: Dependent on the number of solvent molecules, min 12582912 bytes
Keywords: permutation reduction, solvent entropy, all-atom (fully atomistic) molecular dynamics simulations, GROMACS, compacted configuration space density.
PACS: 02.60.Pn, 02.70.-c, 02.70.Ns, 05.10.-a, 87.10.-e, 87.10.Tf, 05.70.-a, 65.40.gd.
Classification: 3, 4.8, 4.9.

External routines: liblap (included); From GROMACS-3.3.1: libgmx (not included)

Nature of problem:
Estimating the entropy of solvent molecules from a molecular dynamics simulation trajectory cannot be performed on ordinary trajectories.

Solution method:
Compacting the configuration space of molecules by exploiting their permutation symmetry. Applies to trajectories either compatible to those obtained with the GROMACS simulation package [1] or multi-model pdb (Protein Data Bank) files.

Restrictions:
In rare cases the time to find a solution for the linear assignment problem can be very long.

Running time:
Dependent on trajectory length and number of molecules to be permuted.

References:
[1] van der Spoel, D. et al., J. Comput. Chem. 26 (2005) 1701.