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

[Justin Lemkul]

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

-- 
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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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