On Fri, Mar 23, 2018, Dmitry Suplatov wrote:
>
> I have been recently wondering about benefits of the AMBER program compared
> to other software solutions (e.g., NAMD, Gromacs).
Your email arrived at a very busy time (we are preparing for a big
release), and has no simple answers. I'll try to make a few comments
below.
> 1. My understanding is that AMBER is not the fastest implementation, i.e.,
> the GROMAC's GPU version of classical MD is significantly faster, right?
Sigh...comparing implementation speeds could be a full-time job. One
thing to remember is that Amber's GPU code (pmemd.cuda) does almost all
of the calculation on the GPU, so that performance is almost entirely a
function of which GPU one is using, and does not depend on having a
high-performance (or expensive) CPU. There are lots of benchmarks at
the GPU page of ambermd.org: I hope these may be of some help.
>
> 2. What about the implementation of the force fields?
> - Both GROMACS and NAMD support the AMBERFFs, is there any difference in
> how they do it compared to the original AMBER?
If you click on the "Force Fields" tab at ambermd.org, and scroll to
the bottom, you will see lots of links about using the Amber force field
in other programs. Suggestions, updates and corrections to the
information there are really welcome--it's hard to keep all this stuff
up to date.
...hope this helps....dac
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Received on Tue Mar 27 2018 - 07:00:02 PDT
