[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 A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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