[gmx-users] Re: what do Coul-SR, LJ-SR, Coul-14 and LJ-14 mean in g_energy

Justin Lemkul jalemkul at vt.edu
Tue Feb 12 18:00:51 CET 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list