[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?
Justin Lemkul
jalemkul at vt.edu
Thu Aug 15 15:08:11 CEST 2013
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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