Re: [AMBER] FW: Regarding AMBER 14

From: praSanna kuMar naYak <>
Date: Wed, 12 Aug 2015 16:56:51 +0530

Thanks for the info Jason.

-----Original Message-----
From: Jason Swails []
Sent: 12 August 2015 16:31
To: AMBER Mailing List <>
Subject: Re: [AMBER] FW: Regarding AMBER 14

On Wed, Aug 12, 2015 at 3:04 AM, praSanna kuMar naYak <> wrote:

> If I'm going to install serial and parallel version of AMBER14 in
> different directories, so how to make use $AMBERHOME? Is it like to
> set every time you want to use either versions of MABER14. Please
> suggest which one make default AMBERHOME ?

​I don't understand why you are going to do this. The serial and parallel versions of all of the programs have different names (e.g., the serial sander is called "sander" and the parallel one is called "sander.MPI").
Maintaining separate installations of *only* parallel and *only* serial in different directories seems unnecessarily complicated, with no real benefit for doing so. [1]

​What's more is that some parallel programs actually depend on serial ones. For example, uses serial sander, cpptraj, and nab to run its calculations.

So my advice is just follow the instructions in the manual and install them all in the same directory. If you simply can't do that for some reason, then in general I think it's more important for the serial versions of the programs to have AMBERHOME set than for the parallel versions. But that's inviting potential problems and is *not* a supported split. So if you start having strange problems, one of the first suggestions will be to install both serial and parallel in the same place.


[1] The only counterexample I can think of is when an HPC environment is trying to support more than one MPI. But for Amber, it would just be easier to install both serial and parallel programs in each of the installation directories and deal with the slight duplication.

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Aug 12 2015 - 04:30:04 PDT
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