[gmx-users] neighbor list

[Sikandar Mashayak]

Thanks Mark. That helps.

--
Sikandar


On Mon, Jul 28, 2014 at 1:58 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> On Mon, Jul 28, 2014 at 8:27 PM, Sikandar Mashayak <symashayak at gmail.com>
> wrote:
>
> > Hi,
> >
> > I need to set up a simulation of LJ system, such that neighbor list is
> > built using grid algorithm with a cut-off of lj_cut_off + 0.1 every 20
> > timesteps.
> >
>
> So, you want a single-range scheme with an explicit buffer. This will be
> faster if you use the Verlet scheme in GROMACS >= 4.6, not the group
> scheme. Even more so if that will let you use a GPU...
>
>
> > So I am wondering what should be the accurate settings in the grompp.mdp
> > file.
> >
> > After reading the manual, I understand rvdw must be >= rlist.
>
>
> No, that'll get you a twin-range scheme.
>
> So how can I
> > specify rlist=lj_cut_off+0.1, should I use rlistlong?
> >
>
> nstlist
> rlist = rvdw + 0.1
>
> and to force mdrun to use your explicit buffer (rather than tune the buffer
> size automatically)
>
> verlet-buffer-tolerance = -1
>
> Also, the cut-off scheme 'group' for simple LJ atoms with no charge, is it
> > equivalent to building neighbor list using atoms rather than group, since
> > each charge group will have only a single atom?
> >
>
> Yes, so long as that is what your input topology specifies. "Charge groups"
> can be specified even though all the charges are zero, and obviously you
> don't want to do this! However, using the Verlet scheme means they're
> always ignored anyway.
>
> Mark
>
>
> >
> > Thanks,
> > Sikandar
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