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
amber10/test/full_pimd/Run.full_pimd.
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
yet.
Sincerely,
Wei
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
>working?
>
>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
>Ross
>
>/\
>\/
>|\oss Walker
>
>| HPC Consultant and Staff Scientist |
>| San Diego Supercomputer Center |
>| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
>| http://www.rosswalker.co.uk | PGP Key available on request |
>
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>
Received on Wed Apr 25 2007 - 06:07:33 PDT
