[gmx-developers] triggering GMX_NB_GENERIC produces wrong interactions
Igor Leontyev
ileontyev at ucdavis.edu
Tue May 11 10:44:43 CEST 2010
>> Dear gmx-developers,
>> I would like to test non-standard nonbonded interaction which can not be
>> implemented simply defining tables.
>
>If the interactions are pairwise, being unable to use tables sounds
>wildly unlikely. If you discuss your idea, you may learn about a good
>way to do it :-)
>
>> According to posts on gmx-developers
>> board, the simplest way to do this is to modify "gmx_nb_generic_kernel"
>> subroutine. To make use the routine the environment variable
>> GMX_NB_GENERIC should be set up. The energy comparison obtained with "set
>> GMX_NB_GENERIC=0" and without, however, produces different energies.
>> What can be done?
>
> It's probably immaterial, but setting GMX_NB_GENERIC to 1 is a better
> idea.
I didn't find any description of meaning of specific values of
GMX_NB_GENERIC. But setting GMX_NB_GENERIC to even "3D1" produces the same
result. BTW, may there be any relation between my issue and the problem
reported here some time
ago?
http://oldwww.gromacs.org/pipermail/gmx-developers/2009-July/003505.html
>
> Look further back in the .log file to see what mdrun is reporting about
> what nonbonded routines it is using.
>
> Life will probably be easier if you do your development and initial
> testing work on a single processor.
Sure, but the behavior of serial versions in this particular test is exactly
the same.
>
> You shouldn't be using PME, because it requires a particular form for
> the nonbonded interactions... (unless that's the target of your test)
Thank you for extended comments. Am I correctly understand a hierarchy of
programming efforts? The simplest (but computationally slowest) option
utilizes gmx_nb_generic_kernel subroutine; intermediate option is to modify
and use nb_kernelXXX routines (without assembly loops) and the scary option
is to modify kernel routines written on assembler? What is the approximate
ratio between computation times of these 3 routines?
>
> Mark
>
>> The system is equilibrated box of 216 SPC/E water molecules. Initial
>> temperature, LJ (SR) and Coul. recip. energy terms are the same, while
>> Coulomb (SR) term differs essentially. See bellow output of step 0.
>>
>> openmpi/mpirun -np2 mdrun -s water216.tpr
>> ======================================================
>> There are: 648 Atoms
>> Charge group distribution at step 0: 112 104
>> Grid: 4 x 3 x 3 cells
>>
>> Constraining the starting coordinates (step 0)
>>
>> Constraining the coordinates at t0-dt (step 0)
>> RMS relative constraint deviation after constraining: 0.00e+00
>> Initial temperature: 295.174 K
>>
>> Started mdrun on node 0 Mon May 10 22:43:13 2010
>>
>> Step Time Lambda
>> 0 0.00000 0.00000
>>
>> Energies (kJ/mol)
>> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
>> 1.73768e+03 -1.04948e+04 -1.13345e+03 -9.89062e+03 1.58418e+03
>> Total Energy Temperature Pressure (bar)
>> -8.30643e+03 2.94714e+02 -9.93848e+02
>>
>> ======================================================
>>
>>
>>
>> export GMX_NB_GENERIC=0
>> openmpi/mpirun -np2 mdrun -s water216.tpr
>> ======================================================
>> There are: 648 Atoms
>> Max number of connections per atom is 2
>> Total number of connections is 864
>> Max number of graph edges per atom is 2
>> Total number of graph edges is 864
>>
>> Constraining the starting coordinates (step 0)
>>
>> Constraining the coordinates at t0-dt (step 0)
>> RMS relative constraint deviation after constraining: 0.00e+00
>> Initial temperature: 295.174 K
>>
>> Started mdrun on node 0 Mon May 10 22:25:39 2010
>>
>> Step Time Lambda
>> 0 0.00000 0.00000
>>
>> Grid: 3 x 3 x 3 cells
>> Energies (kJ/mol)
>> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
>> 1.73768e+03 4.18426e+04 -1.13345e+03 4.24468e+04 1.58623e+03
>> Total Energy Temperature Pressure (bar)
>> 4.40330e+04 2.95095e+02 2.00676e+05
>> ======================================================
>>
>> Igor
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