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

From: Wei Zhang <>
Date: Mon, 30 Apr 2007 11:32:19 -0500

Francesco Paesani wrote:

> Hi Ross,
> It sounds good to me. I'm in the process of putting the QMMM/PIMD test
> cases in test/PIMD using the updated version of PIMD/CMD.
> However I have a question for you.
> How did you check that the old PIMD with QMMM results were actually
> correct? Do you have your own PIMD code coupled to QMMM? For all other
> PIMD tests I checked the amber results against the results I obtained
> with my own code, but for the PIMD/QMMM results this is not possible
> for me since the i don't have any QMMM code. Checking against the old
> tests does not make any sense since some of the PIMD/CMD stuff has
> been changed and, as a consequence, the resulting outputs will be
> different.
> Thanks,
> Francesco

Hi Francesco,

I prepared the PIMD/QMMM test cases for amber9. I think we can validate
the new code by comparing
its result to amber9 code. I think we can run the following tests to
validate it:

First of all, the energy after the first step should be the same for two

Secondly, if ntt is set to 0, then the energy of the other steps should
be same.

Finally, for ntt equals 3, the energy won't match because the random
number sequence is different,
but if we can change one code to re-ordering the random number, we
should be able to get the same
energy for two codes.



> 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 |
>> | San Diego Supercomputer Center |
>> | Tel: +1 858 822 0854 | EMail:- |
>> | | PGP Key available on request |
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Received on Wed May 02 2007 - 06:07:18 PDT
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