On 5/17/12 3:32 PM, Lara Bunte wrote:
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).
I just want to clarify something, though it isn't even really relevant, perhaps
it will be instructional. The 1/length issue does not mean the potential is
calculated from 1/r. In fact, neither is a Coulombic potential, though it is
proportional to this factor. The issue that was initially raised was to help
you understand that force constants for bonds must have a length term in the
denominator of the units, i.e. a 1/length (to some power) dependence.
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?
I would suspect so. One cannot have a bond force constant that is not have a
length term in the denominator. Presumably the true units are kcal/(mol A^2),
which can be easily converted to kJ/(mol nm^2) for use in Gromacs.
-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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