[gmx-users] Re: Simulation of 2D lattice model

Justin Lemkul jalemkul at vt.edu
Sat Jan 5 19:18:33 CET 2013

On 1/5/13 1:45 AM, James Starlight wrote:
> Justin, thanks for explanation again!
> So if I understood correctly in the  ffnonbonded c6 correspond to the
> attraction term and c12 to the repulsion term doestn't it ?  So might


> the vdw radius of the atom be increased/ deacreased via corrections in
> the c6 term ?
>              mass charge ptype       V(c6)      W(c12)
>   O    8 15.99940  0.000     A 0.22617E-02 0.74158E-06

Both C6 and C12 are calculated from both epsilon and sigma, so it's not clear to 
me that simply tweaking C6 alone would somehow be considered changing the van 
der Waals radius.

> by the way I've found that in all gromos ff both C6 term given in the
> inapropriate form
> C    6 	0.000      0.000     A  0.0023406244  4.937284e-06
> so it may complicate such correction in that ff.

What's wrong with it?



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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