[gmx-users] Force Constants and Unit Systems

[Justin A. Lemkul]

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

-- 
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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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