[gmx-users] GROMACS vs NAMD

[Mark Abraham]

> Hii...
>
> Could somebody kindly point out to me the essential difference between the
> simulation procedures between NAMD and GROMACS.

Not really... the general procedure is the same, but the names for things
change a bit.

> I am familiar with NAMD,
> but
> since I am running it on a single processor machine I hear that GROMACS
> would be much more efficient. Is there any comparison of the results
> available on publicly available literature. If so it would be very kind if
> somebody knowledgeable could kindly point that out to me, or send me the
> relevent paper.

I'm not aware that there is one. In general, doing meaningful and fair
comparisons is difficult because the performance of all such codes is
strongly dependent on system size, hardware attributes, which algorithms
you want to use and how much effort has gone into optimizing them. Still,
the general observation that GROMACS will be faster on a single-processor
machine is true. You should try it yourself on your hardware and see.

Mark