[gmx-users] Tabulated potential, derivative errors and interpolation
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jan 7 19:16:15 CET 2010
ms wrote:
> David van der Spoel ha scritto:
>> ms wrote:
>>> Hi,
>>>
>>> I am trying to use a tabulated potential but I have a hard time getting
>>> the derivatives right (apparently), which puzzles me.
>>>
>>> I tried at first to use the analytical expression for the derivative,
>>> and I got warnings ranging from:
>>>
>>> "WARNING: For the 2168 non-zero entries for table 1 in
>>> table_10_70_0.4_5_C-alpha_C-alpha.xvg the forces deviate on average 133%
>>> from minu
>>> s the numerical derivative of the potential
>>>
>>> WARNING: For the 257 non-zero entries for table 2 in
>>> table_10_70_0.4_5_C-alpha_C-alpha.xvg the forces deviate on average 300%
>>> from minus
>>> the numerical derivative of the potential"
>>>
>>> to
>>>
>>> "WARNING: For the 268 non-zero entries for table 2 in
>>> table_10_70_0.4_1_C-alpha_C-alpha.xvg the forces deviate on average
>>> 120138% from minus the numerical derivative of the potential"
>>>
>>>
>>> At first I thought it was because I am artificially "cutting" the
>>> highest values of the repulsive term, putting everything above 10^17 as
>>> 10^17 with a derivative of 0, but playing with that didn't help; also I
>>> found that there are errors too in the repulsive part, which hasn't
>>> out-of-range values.
>>>
>>> So I thought it could have been some mysterious error in the math, and
>>> tried estimating it numerically, but again with a numerically-estimated
>>> table I have errors, and even worse ones:
>>>
>>> "WARNING: For the 257 non-zero entries for table 2 in
>>> table_10_70_0.4_5.xvg the forces deviate on average 120773% from minus
>>> the numerical derivative of the potential"
>>>
>>> I used mdrun with -debug 1 to see what tables the guy is actually using,
>>> and I am also concerned, because there is something weird which could
>>> explain the problem: why are *positive* values routinely interspersed
>>> with the right *negative* values in the derivative?
>>>
>>> For example, this is an excerpt of rtab.xvg:
>>>
>>> 3.0992913246e-01 2.7511889648e+02 7.0945126953e+03
>>> 3.1012925506e-01 2.7884115601e+02 -1.2228130859e+04
>>> 3.1032931805e-01 2.7019714355e+02 -6.7522789062e+04
>>> 3.1052938104e-01 2.5448614502e+02 -8.2872140625e+04
>>> 3.1072947383e-01 2.3970016479e+02 -5.8276152344e+04
>>> 3.1092956662e-01 2.3383134460e+02 6.2780151367e+03
>>> 3.1112965941e-01 2.3702958679e+02 -1.0651265625e+04
>>> 3.1132972240e-01 2.2957331848e+02 -5.8167523438e+04
>>> 3.1152981520e-01 2.1604493713e+02 -7.1314695312e+04
>>> 3.1172990799e-01 2.0332643127e+02 -5.0073011719e+04
>>> 3.1192997098e-01 1.9829878235e+02 5.5352783203e+03
>>> 3.1213006377e-01 2.0104492188e+02 -9.2590859375e+03
>>> 3.1233015656e-01 1.9461547852e+02 -5.0073472656e+04
>>> 3.1253021955e-01 1.8298132324e+02 -6.1317703125e+04
>>> 3.1273031235e-01 1.7205114746e+02 -4.2998656250e+04
>>> 3.1293040514e-01 1.6774539185e+02 4.8916777344e+03
>>> 3.1313049793e-01 1.7010066223e+02 -8.0468198242e+03
>>> 3.1333056092e-01 1.6456481934e+02 -4.3058406250e+04
>>> 3.1353065372e-01 1.5456475830e+02 -5.2672746094e+04
>>> 3.1373074651e-01 1.4518064880e+02 -3.6885503906e+04
>>> 3.1393080950e-01 1.4149731445e+02 4.2984921875e+03
>>> 3.1413090229e-01 1.4351583862e+02 -6.9780966797e+03
>>> 3.1433099508e-01 1.3875308228e+02 -3.6990878906e+04
>>> 3.1453105807e-01 1.3016751099e+02 -4.5200566406e+04
>>> 3.1473115087e-01 1.2211988831e+02 -3.1613373047e+04
>>> 3.1493124366e-01 1.1897129822e+02 3.7776948242e+03
>>>
>>> Thank you for help!
>>> Massimo
>> Which gromacs version?
>>
>
> Sorry! 4.0.5
>
I can not reproduce this. Can you give exact command line and details
about the system? vdwtype etc.?
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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