On 11/10/11, Carla Jamous <[email protected]> wrote: > Hi everyone, > > I ran my simulations with these parameters: > > nstlist = 10 > ns_type = grid > rlist = 0.9 > coulombtype = PME > rcoulomb = 0.9 > vdwtype = cut-off > > rvdw = 1.2 > > Apparently, in Gromacs, when using vdwtype = cut-off, > > > > > > pre.cjk { font-family: "DejaVu Sans",monospace; }p { margin-bottom: > 0.21cm; }the potential changes discontinuously. >
The potential as a function of distance between any pair of atoms is discontinuous at the cutoff. > However, I have a constant LJ(SR) energy and a constant LJ(LR) energy, > So your particle density is nearly constant. Particles moving inside the cutoff balance those moving outside the cutoff. A changing value should indicate lack of equilibrium, not whether the cut-off is a significant source of error. > although I didn't use either Switch or Shift. Please can anyone explain how > does the cut-off really works in Gromacs and whether my simulations are > correct or not? > Please see the discussions in the manual for theory. Probably the simulations are fine. Mark > > > > Thanks > > Carla > > >
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