[gmx-users] The meaning of rlist, rvdm and rcolumn
Nuno R. L. Ferreira
nunolf at ci.uc.pt
Mon Aug 2 19:47:49 CEST 2004
----- Original Message -----
From: "Berk Hess" <gmx3 at hotmail.com>
To: <gmx-users at gromacs.org>
Sent: Wednesday, July 28, 2004 2:12 PM
Subject: Re: [gmx-users] The meaning of rlist, rvdm and rcolumn
> I guess there is confusion here because of shifted or switched potential.
> When using cutoff VdW/electrostatics interactions there are two
> options in gromacs (I will use vdw, but the same holds for coulomb):
> rlist = rvdw: this option is clear.
> rlist > rvdw: twin-range/twin-cutoff method, forces beyond rlist are only
> updated every nstlist steps.
Did you want to say, rlist < rvdw in this case (cutt-off)?
> When using shifted or switched interactions you want to have:
> rlist > rvdw
> such that pairs of atoms do not move beyond rvdw while the neighborlist is
> not updated.
> Before 3.2 Gromacs would not allow rlist > rvdw, but that has been fixed.
> > > So in v3.2, this has been solved. And now the rlist is actually the
> > > neighbor list search cutoff, means rlist=rvdm+shell, rcdm and rcoul
> > > the real cut-off. This is the common method that MD simulation use.
> I would not say that that is the common method.
> It is used often for VdW interactions, but less often for electrostatic,
> it should not be used with for instance PME.
> The Gromos forcefield uses a 1.4 nm cut-off for the VdW interactions,
> in which case there is no need for switching or shifting, the errors are
> Mostly a 0.9/1.4 nm twin-range cut-off is used with this forcefield.
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