[gmx-users] Re: problem of tabulated bonded potential

Z.Xiao zfengxiao at 126.com
Tue Nov 9 13:35:28 CET 2010

XAvier, thanks for your reply.
 the numberical derivative -f'(n)=dy/dx=-(y(n+1)-y(n-1))/(n+1)-(n-1).
so -f'(n)=-(y(n+1)-y(n-1))/2. Is it wrong?

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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