[gmx-users] L-J question

[David van der Spoel]

Anthony Cruz wrote:
> Hi users:
> I have a little question. I found some L-J parameters for heme iron for the 
> GROMOS87 FF and I want to use it in the GROMOS ff43a1 . The units as appear 
> in the paper [biophys. J. 1995 (69) p810] A(kJ nm^ -12 mol ^-1) 4.30115e-5 
> and B (kJ nm^ -6 mol ^ -1) 8.886909e-3.  I need to make any changes to the 
> values there is any convertion factor??

it looks about right, but check the equations in the paper and compare 
to those in the manual.

> 
> Also I found other L-J parameters [J. Phys. Chem. B 2002 (106) p12031] the 
> unit for this other are A[(kcal/mol)/A^12] 10389.5 and B[(kcal/mol)/A^6] 
> 288.3 also appear the fallowing equation Vnb(rij) =Aijrij^ -12 - Bijrij ^ -6 
> with Aij(Bij) the geometric means of Ai and Aj(Bi and Bj).  How I can 
> inplemet this values to use it in the GROMOS ff43a1????
  I think is is default, but check the section about combination rules 
in the manual.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++