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

massimo sandal devicerandom at gmail.com
Fri Aug 16 23:20:07 CEST 2013

On 15 Aug 2013 15:27, "grita" <cemilyigit at arcor.de> wrote

> In short, the sigma is the separation or the 'diameter'. True or False ???

Neither. The diameter of a particle is a meaningless concept here. You have
a continuous potential, not a definite boundary.

If you want your particles to *almost* never come closer than a certain
distance, you need the potential to be positive and much higher than the
average thermal energy at that distance. How to translate this in numbers
depends on your specific needs.

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