[gmx-users] Force Constants and Unit Systems
lara.bunte at yahoo.de
Thu May 17 19:33:37 CEST 2012
>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.
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.
Thanks for helping me
----- Ursprüngliche Message -----
Von: Richard Broadbent <richard.broadbent09 at imperial.ac.uk>
An: Lara Bunte <lara.bunte at yahoo.de>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Gesendet: 19:18 Donnerstag, 17.Mai 2012
Betreff: Re: [gmx-users] Force Constants and Unit Systems
On Thu, 2012-05-17 at 17:58 +0100, Lara Bunte wrote:
> >One cannot convert between these units, since kcal/mol is an energy term, and
> >kJ/(mol nm^2) is a force constant.
> This confuses me, because in the paper where that constants are from is written, I quote:
> "Force constant k in kcal / mol calculated by DFT"
The unit of Force is [Mass]*[Length] /[Time]^2 = [Energy]/[Length] in
any unit system.
Therefore either they have a potential of the form 1/[Length] or they
weren't using the term correctly.
A harmonic bond must have a force constant with units [ Energy ]/
[ Length ]^2 In gromacs this is therefore kJ/(mol nm^2)
The conversion from kcal/mol to kJ/mol is easily found by googling:
> In my parametrization I have this values. Could you please explain this?
> Greetings and really thanks for your help
> ----- 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>
> Gesendet: 18:52 Donnerstag, 17.Mai 2012
> Betreff: Re: [gmx-users] Force Constants and Unit Systems
> On 5/17/12 12:25 PM, Lara Bunte wrote:
> > Hello
> > I never had contact with such units. Could you please help me and explain me
> > how to transform following units:
> > 1.) kcal / mol --> kJ / (mol * nm^2)
> One cannot convert between these units, since kcal/mol is an energy term, and
> kJ/(mol nm^2) is a force constant.
> > 2.) kcal / (mol * rad^2) --> kJ / (mol * rad^2)
> The transformation between kcal and kJ requires a simple multiplication.
> > I have additionally some question to that: Both should be units of a force
> > constant. From Hooke's law F = -kx follows for me, that the unit of a force
> > constant is Newton N over distance m, in S.I. units kg/sec^2 (mass over time
> > square).
> > What is the correspondence between above from Hooke's law and that units of
> > force constants in molecular dynamics simulations?
> Force is also expressed as kJ/(mol nm) - see Chapter 2 of the Gromacs manual.
> Thus, since x is in units of nm (distance), then k has units of kJ/(mol nm^2).
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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