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? Thanks -- View this message in context: http://gromacs.5086.n6.nabble.com/what-do-Coul-SR-LJ-SR-Coul-14-and-LJ-14-mean-in-g-energy-tp4450921p5005471.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
