Re: AMBER: A question on AMBER8 installation

From: Robert Duke <>
Date: Wed, 20 Oct 2004 08:35:00 -0400

Please read the amber 8 manual, pmemd section, first. Then read the README
under amber8/src/pmemd. Finally, look at the web page for
updates about using ifort 8 to compile pmemd 8 (generally stuff with my name
on it on that page pertains to pmemd installation, performance, and mpi
issues). Finally, if you need more info on mpich (I have not been following
this thread so I don't know the details), look at the pmemd 3.0-3.1 release
notes, which have more info on surviving installing mpich (note, some
outdated, and should be read in the context of the later notes about pmemd
8). If you are using mpich, also plan on reading the pertinent parts of
that manual. This stuff is not straightforward for 3 reasons that I am
aware of, and probably others: 1) anything relating to using ifort 8 is
confusing because ifort 8 did not work well with amber 8 (or at all with
pmemd) when amber 8 was released; thus we had to post stuff on the web page
to handle ifort 8 + amber 8, 2) there are a lot of platforms in use out
there, and we don't have them all, and we cannot guess at the various
configuration issues that may exist on those platforms; this is particularly
true in the linux world; linux may be cheap, but the cost comes in the grief
associated with getting the combination of linux release x + fortran
compiler y + c compiler z + mpi implementation x' + hardware y' + (whatever
screwball configuration issues that exist on the given configuration z') to
all actually work; this generally requires a little problem solving at the
installation site, unless you are using exactly a setup we test and
recommend, and 3) the amber development organization is not exactly huge,
with tons of guys devoted to providing this type of user support (so please
read stuff, and don't expect instant nirvana, it sometimes takes me a few
hours to get something running on a new linux configuration).
Regards - Bob Duke

----- Original Message -----
From: "Hwankyu Lee" <>
To: <>
Sent: Wednesday, October 20, 2004 12:12 AM
Subject: Re: AMBER: A question on AMBER8 installation

> Thanks for all the advice. I finally installed AMBER8.
> The first problem was that my linux didn't have X development tool.
> Second problem was that I used icc v8.1. When I installed X development
> tool and used gcc and g++, it was installed without any problem.
> I have one more question about pmemd. I may have to install pmemd
> because there is no pmemd in /amber8/exe/ directory. I wonder if I need
> to go to amber8/src/pmemd/ directory and then use ./configure and make
> install. If so, which options (-**) do I need to use with configure?
> Could you advise me right way to install pmemd?
> Thanks,
> best,
> Hwankyu.

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Received on Wed Oct 20 2004 - 13:53:00 PDT
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