[gmx-users] The meaning of rlist, rvdm and rcolumn

[Berk Hess]

>From: "Nuno R. L. Ferreira" <nunolf at ci.uc.pt>
>Reply-To: "Nuno R. L. Ferreira" <nunolf at ci.uc.pt>,Discussion list for 
>GROMACS users <gmx-users at gromacs.org>
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] The meaning of rlist, rvdm and rcolumn
>Date: Mon, 2 Aug 2004 18:47:49 +0100
>
>----- 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
>are
> > > > 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
> > negligible.
> > Mostly a 0.9/1.4 nm twin-range cut-off is used with this forcefield.
> >
> > Berk.
> >
> > _________________________________________________________________
> > MSN Search, for accurate results! http://search.msn.nl
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
> >
>
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-request at gromacs.org.

_________________________________________________________________
Play online games with your friends with MSN Messenger 
http://messenger.msn.nl/