Hi Lara, On Thu, 2012-05-17 at 17:58 +0100, Lara Bunte wrote: > Hi > > > >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: Which paper? > > "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: kcal/mol Richard > > > In my parametrization I have this values. Could you please explain this? > > Greetings and really thanks for your help > > Lara > > > > > > ----- Ursprüngliche Message ----- > Von: Justin A. Lemkul <[email protected]> > An: Lara Bunte <[email protected]>; Discussion list for GROMACS users > <[email protected]> > CC: > 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 > > -- > ======================================== > > 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
