[gmx-users] problem of tabulated bonded potential

XAvier Periole x.periole at rug.nl
Tue Nov 9 09:02:04 CET 2010

On Nov 9, 2010, at 7:12 AM, Z.Xiao wrote:

> Dear all gmxers,
> I meet some problems when I use the tabulated bonded potential.
> My original function is a sum of An*cos(x)^n (n=1-8).For short here  
> I replaced it by cos(x).
> if f(x)=cos(x),then -f'(x)=sin(x).and the numberical derivative - 
> f'(x)=-(y(n+1)-y(n-1))/2.
here you should have dy/dx, re you really doing this?
> but there are great discrepancy between the two -f'(x).
> which is right?
> and if mdrun with the derivative of original function I would met a  
> warning:the forces deviate
> on average 207% from minus the numerical derivative of the  
> potential.but mdrun with the the
> numberical derivative there is no warning.
> -- 
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