[gmx-developers] [Fwd: coulomb SR in 3.3cvs]

[David van der Spoel]

On Mon, 18 Jul 2005, Michel Cuendet wrote:

>
>Hi,
>
>I subitted this message already on the gmx-users mailing list, but got no
>feedback. I think it's an important issue for the CVS version 3.3. In the
>meantime, I could reproduce the problem on xeon cpus, so it's not itanium specific.

Are these all the energies? No LJ-LR?
Are you running pressure coupling? If so check differences there as well.

Do also check the revisions page.

>
>Here is the original message :
>--------------------------------------------------------------------------------
>
>I compiled the 3.3 CVS version of 27.05.2005 on itanium2 with the intel
>8.1 compiler. (for those who don't know, the cvs version brings a
>terrific speedup on itaniums). Tests were performed with both versions
>in double precision.
>
>I compared the different energies obtained with 3.2.1 and 3.3, by taking
>the same trr (from a 3.2.1 equilibration, 85000 atoms, PME) and running
>it with both versions for about 12ps. From the tables below, one sees
>that there is a gap between Coulomb (SR) of 3450 KJ/mol, and between
>potential energies of  3280 KJ/mol.
>
>A close inspection of the energy files reveals that the version 3.3
>reproduces the same energy as 3.2.1 at the first step, but the system
>relaxes very quickly (0.5ps) to a lower energy with 3.3.
>
>Rerunning with 3.3 the trajectory produced by 3.2.1 surprisingly gives
>the correct energies.
>
>Any explaination for that ?
>
>Thanks,
>Michel
>
>
>3.2.1 :
>
>Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
>
>-------------------------------------------------------------------------------
>
>G96Bond                      6723.8    140.873    138.612   -6.69756   -87.0817
>
>G96Angle                    10213.6    173.746    173.579    2.02771    26.3642
>
>Proper Dih.                 4446.16    89.4129    84.2042    8.01199    104.172
>
>Improper Dih.               3264.55     78.886    78.3318   -2.48685    -32.334
>
>LJ-14                       852.608     79.621      79.52     1.0681    13.8874
>
>Coulomb-14                  62903.9    126.041    122.079   -8.35397   -108.618
>
>LJ (SR)                      166906    1099.22     1099.1   -4.19132   -54.4955
>
>Coulomb (SR)             -1.2043e+06    1629.38    1629.34    -3.3074   -43.0028
>
>Coulomb (LR)                -188686     91.952    90.6651    4.08445     53.106
>
>Potential                -1.13768e+06    1031.78    1031.12   -9.84429   -127.995
>
>3.3 CVS
>
>Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
>
>-------------------------------------------------------------------------------
>
>G96Bond                     6486.57    122.559    120.492   -7.32269   -77.6351
>
>G96Angle                    10003.9    152.062    152.054  -0.496268   -5.26144
>
>Proper Dih.                 4391.87    83.2508    80.8574    6.47554    68.6537
>
>Improper Dih.               3194.22    78.6896    78.6495   0.819815    8.69168
>
>LJ-14                       833.553    76.0076    75.8776   -1.45206   -15.3947
>
>Coulomb-14                    62899    124.539     123.82   -4.36711   -46.3001
>
>LJ (SR)                      167720    1182.33    1157.55    78.6782    834.146
>
>Coulomb (SR)             -1.20775e+06    1897.76    1850.85   -137.014   -1452.62
>
>Coul. recip.                -188746     100.09    100.079    0.48938    5.18841
>
>Potential                -1.14096e+06    1149.25    1132.33   -64.1897   -680.539
>
>
>

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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