On 11/28/12 4:38 AM, fatemeh ramezani wrote:
hello
I want add Au-S parameter for E(bond)=K*(r-r0)^2 to bonded parameters of OPLSAA
forcefield. according to the paper, r0=2.4 A , k(au-s)=4180 [kJ/(mol/Å2)]. But
in Gromacs manual K unit is KJ/mol. I dont understand it.
Energies are kJ/mol. Force constants are kJ/(mol-nm^2). Refer to the form of
potential energy for a harmonic bond and the units become clear.
for use of k(au-s), should I unitless it or not? meaning, I should multiple
this K to sigma(au-s) and then put in bonded file?
thank you
All you need here is proper unit conversion (A - nm). Mind the square term
(A^2 - nm ^2), which people often forget.
-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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