Re: amber-developers: State of PIMD / NEB test cases.

From: Francesco Paesani <>
Date: Tue, 08 May 2007 17:48:52 -0600

hi ross and wei,

i just updated the tests for PIMD/NMPIMD/CMD and NEB. Everything is in

so, i think that the following tests can be removed:

tests for pimd_gb and qmm2+pimd are still missing. for these i need your
help because i do not how to generate the proper prmtop files to run
with the new implementation of PIMD within sander.MPI.


Ross Walker wrote:
> Hi Francesco and other PIMD people...
>> Some of the updated PIMD test cases are in the directory
>> test/PIMD and
>> these are included in the Makefile. I'm going to put also there the
>> tests for PIMD/QMMM and PIMD/GB.
> Okay - so let me confirm the situation here...
> 1) All active Amber 10 PIMD test cases are now in the directory
> 2) All active Amber 10 evb test cases are in the directory
> $AMBERHOME/test/evb
> Is this correct?
> If so then I assume all of the following test cases are defunct and can be
> removed from the CVS tree:
> test/evb_bond_umb
> test/evb_bond_umb_nmpimd_nhc
> test/evb_cnst
> test/evb_exp
> test/evb_gauss
> test/evb_morsify
> test/evb_nrg_map
> test/evb_nrg_umb
> These all look to be empty directories so should probably just be backed up
> and removed from the master CVS tree by Dave C.
> test/full_pimd (and all sub directories)
> test/part_pimd (and all sub directories)
> test/pimd_gb
> test/pimd_helium
> test/pimd_ntp
> test/pimd_spcfw
> test/pimd_water
> test/pimd_water_nhc
> These still contain a large number of active CVS files and were the original
> source of my confusion. I suggest all the files get removed from CVS. Dave C
> can then backup the attic files and delete the directories from the master
> cvs tree.
> test/neb_gb
> test/qmmm2/neb_gb
> test/qmmm2/neb_pureQM_PM3
> test/qmmm2/pimd_gb
> test/qmmm2/pimd_pme
> These all still have active CVS files in but are not run from the Makefile
> anymore. This of course means that the code would appear to have been
> updated but we now have no active PIMD QMMM test cases. In addition we
> actually have NO active NEB test cases either QMMM or classical.
> So I assume the above should also be deleted and then Francesco you will
> create verified (and I do mean verified, not just copies of the output
> files, but calculations where you explicitly verify the results) copies of
> QMMM PIMD test cases in the test/PIMD directory?
> Meanwhile since we have no active NEB test cases and I am in the process of
> trying to explicitly verify the NEB results - by checking that it gets the
> correct pathway for alanine dipeptide - I will create a directory called:
> test/NEB/
> and in here I will put a series of classical and QMMM NEB test cases and
> these can become the master NEB test cases.
> Are we all in agreement here?
> If so then I will start going through and cleaning up the above named
> directories using "cvs remove"
> All the best
> Ross
> /\
> \/
> |\oss Walker
> | HPC Consultant and Staff Scientist |
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Received on Wed May 09 2007 - 06:07:35 PDT
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