The GROMACS and NAMD Software Packages Comparison
Armen H. Poghosyan 1*, Grigor A. Yeghiazaryan 1, Hrant H. Gharabekyan 1, Aram A. Shahinyan 11 The International Scientific-Educational Center of the National Academy of Sciences of Armenia, Marshall Baghramian Ave. 24d, 375019 Yerevan, Republic of Armenia.
Received 26 July 2005, Accepted (in revised version) 20 November, 2005
Communicated by Dietrich Stauffer
The comparable feature analysis of NAMD and GROMACS molecular dynamics packages has been done. The benchmarks of 72 and 128 Dipalmitoylphosphatidylcholine (DPPC)/water have been constructed using a cluster (3GHz-Xeon processors and Myrinet network) and the comparison has been performed using GROMOS87 and CHARMM27 force fields modified for lipids with GROMACS and NAMD software packages, respectively. The GROMACS has been displayed as faster than NAMD, likely due to united-atom character of GROMACS and good implementation features. The GROMACS reaches saturation and goes to the worst results, the reason of which is that the program spends more time on communications between processors.
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Key words: NAMD; GROMACS; molecular dynamics; phospholipid bilayers.
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Correspondence to: Armen H. Poghosyan , The International Scientific-Educational Center of the National Academy of Sciences of Armenia, Marshall Baghramian Ave. 24d, 375019 Yerevan, Republic of Armenia. Email: firstname.lastname@example.org