[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?

[Justin Lemkul]

On 8/15/13 8:58 AM, grita wrote:
> Hi,
>
> with "interaction diameter" I mean the following:
>
> I have two spheres with a radii of 2.5 angstrom.
> The spheres should not overlap.
>
>>From that, I derive my 'interaction diameter'/'interaction distance' 5
> angstrom.
>
> Now, the 5 angstroms should be the \sigma in the following formulas
>
>> c^6 = 4 \epsilon \sigma^6
>> c^12 = 4 \epsilon \sigma^12
>
> Is it so?
>

It's still not entirely clear.  Is the value of the LJ potential zero when the 
two spheres are at a 5-A separation?  If it is, then that's the value of sigma. 
  If the 5-A separation defines the energy minimum for the interaction between 
the two particles, then that's not sigma, the 5 A value would be r_m, from which 
sigma can be calculated.  None of this guarantees that the spheres will not 
overlap, given the form of the LJ potential.

-Justin

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Justin A. Lemkul, Ph.D.
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