Dear Grita,
\sigma in gromacs is the value of \sigma in a Lennard-Jones (LJ)
potential defined by:
4\epsilon*[(sigma/r)^12-(sigma/r)^6],
where r is the separation between the two point particles, epsilon is
the well depth, and \sigma is a length scale which characterises the
interaction between two particles. This is the same as in the wikipedia
article Justin linked to or numerous other websites, journal articles,
and text books discussing the LJ potential.
The particles if they have sufficient energy can move closer than \sigma
together or they can move further apart than \sigma.
As Justin said there is no such thing as a particles diameter in gromacs
everything is a point particle with no radius or diameter.
If you want something where the particles absolutely cannot overlap
regardless of their energy you will need to consider hard-sphere
potentials. However, as these are not continuous and therefore not
really suited to MD simulations I doubt that's what you want.
Richard
On 15/08/13 14:26, grita wrote:
Hi Justin,
yes, the LJ potential is zero when the two spheres are at a separation of 5
angstrom.
So, I can be sure, that in this case the \sigma in
c^6 = 4 \epsilon \sigma^6
c^12 = 4 \epsilon \sigma^12
are the seperation or 'my interaction diameter / interaction distance'???
I've asked for this, because in other force fields there are different
definitions of sigma.
Sorry for the confusion.
In short, the sigma is the separation or the 'diameter'. True or False ???
Best, grita
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