[gmx-users] Re: problem of tabulated bonded potential
x.periole at rug.nl
Tue Nov 9 14:07:51 CET 2010
On Nov 9, 2010, at 1:35 PM, Z.Xiao wrote:
> 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?
Depends on how your x is varying.
> 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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