my question is: can I make these atoms closer with creating a larger number of atoms?! for example, I increased the number density in lattice fcc command, but I get the larger Lattice spacing, so in spite of increasing the number density and reducing region, again I generate the atoms that a few of them are far ( 3-4 sigma) from each other! I appologize that I could not explain my question well.
You can certainly create a lattice of atoms with any spacing
you want via the lattice command, e.g. so that nearest
neighbors are less than 1 sigma apart. Then such
pairs would be valid for FENE bonds. Or you can use
different (non-standard) params for the FENE coeffs and
make bonds of any equilibrium length you want. I suggest
you viz the lattices you create. See the lattice doc page
command for info on how to set the density to an arbitrary
value (hence the spacing between individual particles).
Steve