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

[XAvier Periole]

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.
> >
> >
> > --
>
>
>
>
> --  
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search 
>  before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists