Re: Urey-Bradley term

From: Cosmin ROMAN (
Date: Wed Nov 19 2003 - 04:05:27 CST


I am trying to build a tool that finds charmm force field parameters for
carbon nanotubes. It is based on running namd in a loop with a dft program.
CNTs in particular are very difficult to fit and I need all charmm's
parameters to do the job. Namd computes internally the Urey-Bradley terms and
it is a waste of information not to display it. I did a Tcl script but it's
too slow, and I won't have the time to do it in C.

Can namd developers help me in this matter, and build a patch for namd-2.5
that simply displays the ANGLE term split in ANGLE and UREY-BRADLEY terms. I
would have done it myself but to be honest I never was able to compile namd
and that is because of the cvs system.

Thank you,
Kind Regards,

On Wednesday 19 November 2003 01:24, Fangqiang Zhu wrote:
> Unfortunately, NAMD can't display the breakdown of the angle energy. In
> principle you could calculate it from the trajectory, but it will be very
> complicated
> if you want that energy for the whole system...
> Zhu
> Cosmin ROMAN wrote:
> > Hello,
> >
> > Can namd display the Urey-Bradley contribution to the ANGLE energy? As it
> > is, it only displays the sum, i.e. Ktheta(Theta - Theta0)**2 + Kub(S -
> > S0)**2, and I would really like to have them separately.
> >
> > Thanks,
> > Cosmin.

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