Hi I have two questions left:
1.) You wrote >If your term in question is an angle potential, then the force constant should >indeed have units of energy Could you please explain this? Why is it here consistent to have Energy as unit for a force constant? 2.) The force constant is divided by mol. What is the reason for this? In example Energy/length^2 is the force constant, why do we consider Energy/(mol * lenght^2) ? Thanks for helping me Greetings Lara ----- Ursprüngliche Message ----- Von: Justin A. Lemkul <jalem...@vt.edu> An: Lara Bunte <lara.bu...@yahoo.de>; Discussion list for GROMACS users <gmx-users@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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
