RE: AMBER: combining different versions of AMBER

From: Ross Walker <>
Date: Fri, 21 Jul 2006 13:11:44 -0700

Hi Melissa,
Assuming that you are doing a simulation that uses a feature set that is
supported in all 3 versions (e.g. PME simulation) then you should be fine,
the answers should all come out the same. I wouldn't go earlier than 7.0
though as some of the file formats changed slightly and it may get confusing
with converting prmtop files between old and new formats etc.
My best advice to you however is that if you have access to Amber 9 you
should just consider installing this yourself on all the machines you will
use. Intall it in your own home directory and use this. I recommend that
anybody running simulations with Amber does this unless they explicitly
trust the sysadmin of the machine. I.e. if you are using a centrally
installed program how do you know that the person who installed it ran the
test suite and verified it worked. Did they test it in both serial and
parallel, which bugfixes did they apply, have they modified it in anyway...
Your safest bet is just to put the source code in your home directory on
each different machine and build it on that machine, test it on that machine
and then use this installation on that machine. This gives you control over
the program and will likely save you a lot of heartache.
All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
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From: [] On Behalf Of
Melissa Foley
Sent: Friday, July 21, 2006 12:26
Subject: AMBER: combining different versions of AMBER

AMBER users:
I am about to start a project using AMBER, and the computers that are
available to me have different versions of AMBER available, such that I
might end up using a cocktail of versions 7.0, 8.0, and 9.0 for the same
project. Would this be okay? For example, I would probably use 7.0 and 8.0
for preliminary work (antechamber and xleap), 9.0 for sander, sander.LES,
and PMEMD, and then 8.0 for analysis with ptraj. I have looked at the
manuals and I don't see obvious incompatibilities, but I am wondering if it
dangerous to mix versions like this. Does anyone have experience with such
situations, and advice on how I can avoid problems caused by mixing
Thank you very much for any suggestions.

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Received on Sun Jul 23 2006 - 06:07:14 PDT
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