For treatments that require a non-zero buffer length, like shift and
switch, you do this by setting rlist larger than rcoulomb. Coulomb
should be fine with PME + straight cutoff and the difference for LJ
between nstlist=1 and nstlist=10 I expect will be negligible for a 2fs
timestep. Note that I have never tried shifting or switching in
gromacs, but charmm-like behaviour here seems 100% possible in gromacs.
Here is some stuff from the manual:
"The neighbor search cut-off rlist should be 0.1 to 0.3 nm larger than
rcoulomb to accommodate for the size of charge groups and diffusion
between neighbor list updates."
"The neighbor search cut-off rlist should be 0.1 to 0.3 nm larger than
rvdw to accommodate for the size of charge groups and diffusion
between neighbor list updates."
So yes, it is not possible to use a cutoff for coulombic and LJ while
having nstlist>1 and obtaining results that are identical to those
that would be obtained with nstlist=1 (or with sufficient 'buffer').
If you really must do this then set nstlist=1.
Chris.
-- original message --
Usually when we do neighbour searching we should give three
parameters: cut-off distance, buffer length and
the frequency of the neighbour list updating. But in Gromacs *.mdp
file it's just required to give rlist,nstlist,
rvdw and rcoumlomb. Where is the buffer length of neighbour searching
in Gromacs?
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