[gmx-users] L-J question

David van der Spoel spoel at xray.bmc.uu.se
Fri Jun 9 15:55:43 CEST 2006

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 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

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