[gmx-developers] likely an error in gromacs

[David van der Spoel]

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.


-- 
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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