[gmx-users] Force Constants and Unit Systems
Lara Bunte
lara.bunte at yahoo.de
Thu May 17 21:32:42 CEST 2012
Hi
what I meant was, that if a force constant would have the unit kcal/mol, the corresponding potential will be a coulomb potential and I said that this makes no sense. Springs has a quadratic potential, not a Coulomb Potential, like V(r) = 1/r.
Please have a look on page 45, there you can see what is written in my supporting information (it's in English).
http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&ved=0CG4QFjAJ&url=http%3A%2F%2Fedoc.ub.uni-muenchen.de%2F13660%2F1%2FRieff_Benjamin.pdf&ei=dVC1T_XJJIzO4QTojqXADg&usg=AFQjCNFOxi8Cf2eUshmA9rzPfLPra5u-gw&sig2=79QqmWk3b8LSFlVjey4FFg
Do you think it is a typo?
Greetings
Lara
----- Ursprüngliche Message -----
Von: Justin A. Lemkul <jalemkul at vt.edu>
An: Lara Bunte <lara.bunte at yahoo.de>; Discussion list for GROMACS users <gmx-users at gromacs.org>
CC:
Gesendet: 20:37 Donnerstag, 17.Mai 2012
Betreff: Re: [gmx-users] Force Constants and Unit Systems
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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