On 2/12/13 11:06 AM, escajarro wrote:
Hello all,
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?
Actually, the SR terms are indeed interactions of the polymer with itself. 1-4
interactions are special interactions that occur between atoms separated by 3
bonds. SR stands for "short range," which encompasses all interactions that are
not excluded by that occur within the shortest nonbonded cutoff.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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