[gmx-users] Comparing various MD packages

Sabyasachi Sahoo ssahoo.iisc at gmail.com
Tue Aug 25 20:15:32 CEST 2015

Hello all,
I am interested in comparing various MD packages like LAMMPS, GROMACS,
DESMOND, NWChem, RedMD. I was looking through literature to find any
relevant papers regarding the same and found a paper or two that do so. But
they used different set of bench-marking problem sets, and no single common
benchmark was used to compare all of them.

However I fail to understand, how to draw any common conclusion amongst the
molecular dynamics packages, since they have used different benchmark
problems for every package that they tested on. Though we know that every
molecular dynamics package has different objective and each of them try to
meet different goals, but shouldn't we compare all MD packages w.r.t. same
benchmark problem rather than taking different benchmark problem suitable
to individual MD package. Because at the end of the day, along
with optimizations being done for specific subset of MD problems, all
MD packages are implementing same (or rather similar) set of mechanics
equations with the goal of simulation molecules.

If we were to select any one or two benchmark problem for comparing MD
packages, can anyone please suggest some such good benchmark problems,
since it will be harder for me to narrow down the set of such benchmark
problems, owing to my non-biological sciences background. Any material
related to this topic throwing more light in this direction will be of
great help to me. More insight for its better understanding is also hugely

P.S.: If it is already asked question, or something similar was previously
asked, can you please give me the link for same?

Thanks in advance

Yours sincerely,

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