[gmx-users] harmonic angle potential
David
spoel at xray.bmc.uu.se
Sun Aug 17 11:36:01 CEST 2003
On Sat, 2003-08-16 at 13:35, Michael Patra wrote:
> Dear all,
>
> I wounder whether the harmonic angle potential is implemented correctly in
> Gromacs. Since the potential is supposed to depend only on the angle, the
> computed forces should only try to change that angle. The Gromacs angle
> potential, however, seems to also try to change the bond length. This is seen
> when then bond potential is switched off. (For technical reasons, perhaps some
> bug, mdrun crashes when evaluating an angle when there are no bonds, so one has
> to introduce bonds with a vanishing potential.) One will then see that the
> particles connected by the angle are pushed away from each other.
>
> At the end of this message, you will find a short script that will reproduce
> this behaviour with Gromacs 3.1.4.
>
> Yours faithfully,
>
> - Michael Patra
>
Dear Michael,
that was indeed an interesting test case. If you run an energy analysis
you see that you start out with angle energy (= potential) and that
interconverts with the kinetic energy, the total energy is conserved.
This proves that, first the integration algorithm is accurate, and
second that the force is the (correct) negative derivative of the
energy. You can also do a plot of the angle vs. time and you see that
there are large fluctuations due to the fact that you start out with an
angle of 90 while the equilibrium angle is 120. All fine.
It seems that your question is based on a subtle misunderstanding. The
potential is based on the angle indeed, but the forces act in cartesian
space, not in internal coordinates. The forces are computed as the
derivative of the potential with respect to coordinates. From the angle
vs. time plot you can see that the angle equilibrates towards the
specified value, but from ngmx you see that the bonds get much longer.
This is however correct, for the angle potential implemented in gromacs
(and most other programs), because the bond length is not part of the
potential form.
--
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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