Systematic benchmarking of large molecular dynamics simulations employing GROMACS on massive multiprocessing facilities

Journal of Computational Chemistry

Volumn 32, Issue 4, 2011, Pages 600-606

  Gruber, Christian C ^a   Pleiss, Jürgen ^a  

^a UNIVERSITY OF STUTTGART   (Germany)

Author keywords

benchmark; GROMACS; high performance computing; massive parallel calculations; molecular dynamic simulations

Indexed keywords

BENCHMARK; GROMACS; HIGH-PERFORMANCE COMPUTING; MOLECULAR DYNAMIC SIMULATIONS; PARALLEL CALCULATION;

COMPUTER SIMULATION;

MOLECULAR DYNAMICS;

ARTICLE; COMPARATIVE STUDY; COMPUTER; COMPUTER ANALYSIS; COMPUTER PROGRAM; ECONOMICS; MOLECULAR DYNAMICS; TIME;

COMPUTERS; COMPUTING METHODOLOGIES; MOLECULAR DYNAMICS SIMULATION; SOFTWARE; TIME FACTORS;

EID: 79251524910     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21645     Document Type: Article

References (14)

1. Available at:, accessed on 9th August 2010.
2. Hess, B.,;, Kutzner, C.,;, van der Spoel, D.,;, Lindahl, E.,; J Chem Theory Comput 2008, 4, 435.
3. van der Spoel, D.,;, Lindahl, E.,;, Hess, B.,;, Groenhof, G.,;, Mark, A. E.,;, Berendsen, H. J. C., J Comput Chem 2005, 26, 1701.
4. Essmann, U.,;, Perera, L.,;, Berkowitz, M. L.,;, Darden, T.,;, Lee, H.,;, Pedersen, G., J Chem Phys 1995, 103, 8577.
5. Darden, T.,;, York, D.,;, Pedersen, L., J Chem Phys 1993, 98, 10089.
6. Available at:, accessed on 9th August 2010.
7. Available at:, accessed on 9th August 2010.
8. Available at:, accessed on 9th August 2010.
9. Available at:, accessed on 9th August 2010.
10. Frigo, M.,;, Johnson, S. G., Proc IEEE 93, 2005, 216.
11. Available at:, accessed on 9th August 2010.
12. Available at:, accessed on 9th August 2010.
13. Available at:, accessed on 9th August 2010.
14. Available at:, accessed on 9th August 2010.