Re: amber-developers: State of NEB in AMBER10?

From: Wei Zhang <>
Date: Tue, 24 Apr 2007 10:11:12 -0500

Dear Ross,

In amber 10, you need to use sander.MPI to do NEB simulation.
There is a test case showing how to do this in

Note that NEB is now implemented using multi-sander framework, thus it
should be much faster than amber 9, but it is also limited to replicate
the whole
molecule. There is also a plan to implement NEB under LES framework
which will
allow user to only replicate part of the system. but this part has not
been done



Ross Walker wrote:

>Hi All,
>It seems that someone has removed the sander.PIMD.MPI target from the
>Amber10 makefile and has also commented out all of the test cases. This
>renders NEB simulations in amber10 impossible...
>What is the status of NEB now in amber10?
>Why have all the test cases been commented out?
>I have a number of production NEB simulations I want to run over the next
>month for which I was planning to use the Amber 10 distribution - since the
>performance of the Amber 9 NEB sucks. Can someone please let me know what is
>the current status and when it will be working again / how to get it
>If not can you please let me know the last CVS date on which it worked and
>was verified to give the correct answer so I can check that out.
>All the best
>|\oss Walker
>| HPC Consultant and Staff Scientist |
>| San Diego Supercomputer Center |
>| Tel: +1 858 822 0854 | EMail:- |
>| | PGP Key available on request |
>Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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Received on Wed Apr 25 2007 - 06:07:33 PDT
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