[gmx-users] Re: what do Coul-SR, LJ-SR, Coul-14 and LJ-14 mean in g_energy
juan-manuel.castillo at mv.uni-kl.de
Tue Feb 12 17:06:03 CET 2013
I am afraid that, after reading all the documentation I could find about
Coul-SR and LJ-SR, I still do not understand what these terms account for.
I am running a simulation of one single polymer chain in water. My values
for cut-off radious are rlist=rcoulomb=rvdw=1.5, I am using PME for
calculation of electrostatics, and simple cut-off potentials without tail
corrections. My simulation box is large enough, so that the polymer chain
can not 'feel' its periodic images. Nevertheless, the terms
Coul-SR:Polymer-Polymer and LJ-SR:Polymer-Polymer are not zero, as I would
expect if they were the (short-range) interaction of one polymer chain with
a different one. It is also not the short-range interaction of the polymer
with itself, as they are also different from the terms
Coul-14:Polymer-Polymer and LJ-14:Polymer-Polymer energies. Are then the SR
terms equal to the 14 terms plus the exclusion terms? If not, what energy
contributions contain the SR terms?
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