Re: How to obtain the system force on a fixed atom

From: Axel Kohlmeyer (
Date: Tue Dec 22 2009 - 03:34:27 CST

On Mon, Dec 21, 2009 at 4:18 PM, <> wrote:
> Dear Jerome and other NAMD developers,

dear mary,

> I strongly suggest to implement a way to get the system force on a fixed
> atom (not the "zero" value, but the force calculated due to molecular

if you want this feature _that_ desperately, why don't you use a software
package like LAMMPS, that has much more features for introspection
of simulation data? it is also not clear to me, what the distinction between
the "zero" value and system force is that you are pointing out.
the way how you "fix" atoms in an MD simulation is strictly speaking not
a constraint, you either just ignore them during the MD propagation
or set their forces and velocities to zero.

> interactions). This is extremely usefull for calculating the ion diffusion
> constant inside an ion channel. Using harmonic restraint may introduce

i am curious to learn how you can compute the (self) diffusion constant
from the force auto-correlation. i always thought that would give you
access to friction related properties. the self-diffusion would instead be
obtained from the velocity auto-correlation (but usually more conveniently
through mean squared displacement and the einstein relation).

> artificial oscillation behariors for the random force autocorrelaton
> function calculations.

please keep in mind that those oscillations can be controlled via
the mass of the restrained particles and the restraining force constant.
as long as the resulting resonance frequency does not couple to
the frequency spectrum of your system, its effect is negligible relative
to the many, many other systematic errors that a classical MD
simulation typically has.


> Many thanks,
> Mary

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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