On 5/17/12 1:33 PM, Lara Bunte wrote:
Hi
Therefore either they have a potential of the form 1/[Length] or they
weren't using the term correctly.
But a 1/[lenght] potential, which is a coulomb potential makes no sense for
springs, that have a quadratic potential, like V(x) = 1/2 * k * x^2 of a
harmonic oscillator.
Perhaps you should tell us the bonded term your force constant in question
applies. I don't see how this has anything to do with a Coulombic potential, as
force constants are not involved. The 1/length dependence (in terms of
proportionality, not literally that your energy is calculated as 1/r) is in the
units, e.g. kJ/(mol nm^2) - energy is dependent upon the length of the bond, in
other words, the displacement from the equilibrium value.
If your term in question is an angle potential, then the force constant should
indeed have units of energy, per the manual (Table 5.5). If it is anything
else, there is an error somewhere.
So that means probably, that the writers of the paper did an error. Could
such an error ruin my hole MD? My complete force field parametrization is out
of this paper.
It depends on what the error is, if it exists at all. If it is a simple
typographical mistake, then there's likely no harm. If there is some larger
calculation error, then the force constants may be flawed. We have no way to
know, as you've not said what your bonded term is or what the source of the
parameters is.
The results you obtain in a simulation are only as good as the physical model
itself and the assumptions it makes. If you come to find out that there is some
underlying mistake in the parameterization, I would have little or no faith in
the results. Whether you need to be concerned or not at this point is quit unclear.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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