[gmx-developers] likely an error in gromacs
David van der Spoel
spoel at xray.bmc.uu.se
Sat Aug 19 08:22:28 CEST 2006
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
> 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
see chapter 6 in the manual.
> All the best!
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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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