[gmx-developers] tabulated potential energy=nan for r=0 nm and charged atoms

chris.neale at utoronto.ca chris.neale at utoronto.ca
Mon May 9 17:30:26 CEST 2011

Could you please point me to the file and line number so that I can  
change this to a simple sqrt? If it impacts the timing too much, then  
I may just leave r=r^2 and remake my table to provide values based on  

Thank you very much for your assistance,

Quoting Berk Hess <hess at cbr.su.se>:

> Hi,
> In the innerloop r is calculated as rsquared*invsqrt(rsquared).
> Berk
> On 05/09/2011 04:54 PM, chris.neale at utoronto.ca wrote:
>> Dear Developers:
>> I find that even when tabulated potentials specify f(x)=0 and   
>> -f'(x)=0 for x=0, I still get a coulomb(SR) energy=nan when two   
>> charges occupy the exact same spot.
>> Both the manual 4.5.4 page 151 equation 6.23 and the gromacs_nb.pdf  
>>  tabulated potentials tutorial (   
>> http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials )  
>>  indicate that setting f(x)=0 and -f'(x)=0 for x=0 should lead to  
>> an  energy of zero in this case.
>> Is this a bug or a case of WYSIWYG? Can anybody offer any hints on   
>> where I might start searching through the source code with printf   
>> statements to see where the nan develops? I'm guessing there is   
>> some if(r>0) in the code that doesn't technically need to be there.
>> More information and a test system is available in my users-list   
>> post for which I received no responses:
>> http://lists.gromacs.org/pipermail/gmx-users/2011-May/061140.html
>> Thank you very much,
>> Chris.
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