TY - JOUR
T1 - The GROMACS and NAMD Software Packages Comparison
JO - Communications in Computational Physics
VL - 4
SP - 736
EP - 743
PY - 2006
DA - 2006/01
SN - 1
DO - http://doi.org/
UR - https://global-sci.org/intro/article_detail/cicp/7977.html
KW - NAMD
KW - GROMACS
KW - molecular dynamics
KW - phospholipid bilayers.
AB - <p style="text-align: justify;">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.</p>