On Tue, Apr 21, 2015 at 3:02 PM, Atila Petrosian <atila.petrosian.gmail.com>
wrote:
> Dear amber users
>
> I access to Amber 11 and AmberTools 1.5. I want to install Amber 11 and
> AmberTools 1.5 on CentoS 6.3.
>
> Is there any instruction for this installation?
>
You can *try* the advice here:
http://jswails.wikidot.com/installing-amber11-and-ambertools-1-5
Disclaimer: this is an old page (on the main page it is under the listing
of "Outdated pages"), and I have not
tried building Amber 11 + AmberTools 1.5 in quite some time. It is not a
pleasant experience.
In general, I do not think Amber 11 is worth trying to install.
AmberTools 14 includes sander, so the only thing missing from AmberTools 14
that Amber 11 has is pmemd. The CUDA version included with Amber 11 is
slow (by comparison) and does not run on modern GPU hardware or with modern
CUDA toolkits. In my experience, this renders pmemd.cuda version 11 almost
unusable. So unless you *need* the extra 2x throughput you get with pmemd
over sander, I would suggest foregoing Amber11 altogether and just sticking
with AmberTools 14 and sander (or get an Amber 14 license as well if that's
possible and you need pmemd.cuda). And if you *do* need it, then I suggest
installing AmberTools 14 and then trying to build just pmemd from Amber 11.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Apr 21 2015 - 12:30:04 PDT
