[gmx-developers] likely an error in gromacs
Dongsheng Zhang
dong at pampas.chem.purdue.edu
Sun Aug 20 07:07:34 CEST 2006
On Sat, 2006-08-19 at 19:54 +0200, David van der Spoel wrote:
> Dongsheng Zhang wrote:
> > On Sat, 2006-08-19 at 08:22 +0200, David van der Spoel wrote:
> >> Dongsheng Zhang wrote:
> >>> Dear GMX developers,
> >>>
> >>> I used a user-defined potential for non-bonded interactions. By chance I
> >>> found there was likely an error in potential energy calculation. To make
> >>> the story short, I will just tell you what different tests I have done.
> >>>
> >>> In the test, I calculated the potential energy between one pair by using
> >>> user-defined potential (tabulated potential). The coordinates of these
> >>> two particles are:
> >>> 42.04700 37.95200 42.47800
> >>> 42.99200 37.88300 42.77700
> >>>
> >>> The distance between them is 0.99357250826 (got from my own code), it is
> >>> between 0.992 and 0.994
> >>>
> >>> I varied the tabulated potential to see how gromacs and my own code to
> >>> correspond:
> >>>
> >>> Table one (only relevant part): (To make it simple, I set the second
> >>> derivative term zero)
> >>>
> >>> 0.992 0 0 0 0 0 0
> >>> 0.994 0 0 10 0 0 0
> >>>
> >>> The result from my code is 7.86254128, The result from gromacs (by
> >>> defining energy groups to get the interaction of one pair) is 7.802608
> >>>
> >>> Table two:
> >>>
> >>> 0.992 0 0 0 0 0 0
> >>> 0.994 0 0 100 0 0 0
> >>>
> >>> The result from my code is 7.86254128e+01. The result from gromacs is
> >>> 78.562798, which is not 10 times of 7.802608.
> >>>
> >>>
> >>>
> >>> Could anyone give me a hint what happens in gromacs? Thank you a lot!
> >> have you implemented the same cubic spline interpolation scheme as in
> >> gromacs?
> >> see chapter 6 in the manual.
> >
> > Yes. I did. I have read Chapter 6 in the manual to build the potential
> > table and write my own code. The only reason to set the second
> > derivative term zero is to make the calculation simple and easy
> > checking.
> >
> >
> > If I vary the second derivative term, both gromacs and my own code can
> > responds correctly.
> >
> > Continue the test from my previous email,
> >
> > Table 3:
> >
> > 0.992 0 0 0 0 0 0
> > 0.994 0 0 10 100000 0 0
> >
> >
> > The result from my code is 7.84252826 (the result from table 1 is
> > 7.86254128). The result from gromacs is 7.782593 (the result from table
> > 1 is 7.802608).
> >
> >
> > Table 4:
> > 0.992 0 0 0 100000 0 0
> > 0.994 0 0 10 100000 0 0
> >
> >
> > The result from my code is 7.82892957, the result from gromacs is
> > 7.768992.
> >
> > Table 5:
> >
> >
> >
> > 0.978 1.02249 2.13803 -1.14279 -50.1809 1.30597
> > 213.001
> > 0.98 1.02041 2.12496 -1.12887 -49.3674 1.27435
> > 206.995
> > 0.982 1.01833 2.11201 -1.11514 -48.5688 1.24355
> > 201.17
> > 0.984 1.01626 2.09916 -1.10161 -47.7847 1.21355
> > 195.521
> > 0.986 1.0142 2.08641 -1.08827 -47.0147 1.18434
> > 190.041
> > 0.988 1.01215 2.07376 -1.07512 -46.2587 1.15589
> > 184.726
> > 0.99 1.0101 2.06122 -1.06216 -45.5164 1.12818
> > 179.569
> > 0.992 0 0 0 0 0 0
> > 0.994 0 0 10 0 0 0
> > 0.996 1.00402 2.02419 -1.02434 -43.3685 1.04927
> > 165.004
> > 0.998 1.002 2.01205 -1.01208 -42.6781 1.02431
> > 160.434
> >
> >
> > The result from my code is 7.86254128 (the same as that from table 1).
> > The result from gromacs is 7.212971, which is different from the result
> > from table 1 (7.802608). Table 5 looks a little messy. The key point is
> > that the entries for r = 0.992 and 0.994 is the same as table 1.
> > Therefore I expect that I can get the same result as table 1, but
> > gromacs gives me different results. I hope my test results can give you
> > some clues where gromacs made a mistake or I had made a mistake. If you
> > need more information, please let me know.
> >
> >
> > All the best!
> >
> >
> >
> > Dongsheng
> >
> Please submit a bugzilla and upload the different tables and also a tpr
> file.
>
I just report it. Thank you for help!
> --
> 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://folding.bmc.uu.se
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