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[Licence| Download | New Version Template] aeqa_v1_0.tar.gz(958 Kbytes)
Manuscript Title: g_contacts: Fast Contacts Search in Biomolecular Ensemble Data
Authors: Christian Blau, Helmut Grubmuller
Program title: g_contacts
Catalogue identifier: AEQA_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 184(2013)2858
Programming language: C99.
Computer: PC.
Operating system: Linux.
RAM: ≈ Size of input frame
Keywords: Range search, Molecular dynamics, Decomposition scheme, Gromacs.
Classification: 3, 4.14.

External routines: Gromacs 4.6[1]

Nature of problem:
Finding atoms or residues that are closer to one another than a given cut-off.

Solution method:
Excluding distant atoms from distance calculations by decomposing the given set of atoms into disjoint subsets.

Additional comments:
This is an Open Access program

Running time:
O(Nlog(N))

References:
[1] S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J.C. Smith, P. M. Kasson, D. van der Spoel, B. Hess and Erik Lindahl, Gromacs 4.5:a high-throughput and highly parallel open source molecular simulation toolkit, Bioinformatics 29 (7) (2013)