[gmx-developers] triggering GMX_NB_GENERIC produces wrong interactions

[Berk Hess]

Igor Leontyev wrote:
>>> 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
>
That depends on if you have water molecules.
If so, set GMX_NO_SOLV_OPT in addition to GMX_NB_GENERIC

Berk
>>
>> 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
>