[gmx-users] confused about rcoulomb<=rlist

Michael Shirts mrshirts at gmail.com
Wed Jul 12 18:25:05 CEST 2006

Hi, all-

I admit I've been wondering about this as well -- I was involved in
some of the previous discussions.  It seems like the simplest thing is
to have the real space cutoff be at rcoulomb, and if one wants the
real space cutoff to go out to rlist, then one sets rcoulomb = rlist.
But one is not forced to.    Am I missing something?

I think part of the previous discussion was how to get the best energy
conservation -- Berk argued (correctly, I think -- at least it appears
in agreement with simulations I ran) that setting the real space
cutoff = rlist gives the best energy conservation.  But this is
independent of the question of user control -- I think the user should
be able to choose real space cutoff < rlist, for the reasons David
Mobley lists above.

Michael Shirts
Research Fellow
Chemistry Department
Columbia University

> Message: 8
> Date: Wed, 12 Jul 2006 09:08:01 -0700
> From: "David Mobley" <dmobley at gmail.com>
> Subject: Re: [gmx-users] confused about rcoulomb<=rlist
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>,
>         "Discussion list for GROMACS development" <gmx-developers at gromacs.org>
> Cc: Michael Shirts <mrshirts at gmail.com>, John Chodera
>         <jchodera at gmail.com>
> Message-ID:
>         <bc2c99750607120908k684349ebqe904ff21ba3d256c at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Berk,
> > I have added the check.
> >
> > The problem was that Gromacs did not truncate the potential
> > at rcoulomb with PME, only rlist was used. However rcoulomb
> > was used in the determination of beta.
> > To avoid that people thought that rcoulomb had an effect
> > on the cut-off, I have added the check.
> OK, so, in other words, rcoulomb now only affects beta with PME; rlist
> is used for the electrostatic cutoff.
> Is there a straightforward way this could be changed in future
> versions so that the cutoff used for electrostatics could be different
> from rlist? In particular, I am concerned that this means that one
> can't vary the vdw cutoff independently of the electrostatics cutoff
> beyond some limit. That is, rlist needs to be >rvdw with shift/switch
> vdw potentials:
> WARNING 1 [file equil_constp0.7.mdp, line unknown]:
>   For energy conservation with switch/shift potentials, rlist should be 0.1
>   to 0.3 nm larger than rcoulomb/rvdw.
> Suppose I want to run with a 1.4 nm rvdw -- then I now have to use
> rlist=1.5 nm and rcoulomb=1.5 nm? That doesn't seem good. One would
> like to be able to change rvdw independently of the electrostatics --
> for example, to explore the effects of long range van der Waals
> cutoffs. In fact, Michael Shirts and I and others had been trying to
> do exactly that in GROMACS 3.1.4 and 3.3 (adjust rvdw and rlist
> independently of rcoulomb in binding free energy calculations, in
> order to see how strongly the choice of vdW cutoff affects computed
> binding free energies). If changing rlist also changes the real space
> cutoff for electrostatics, things are substantially more complicated
> and it seems unclear how to even address this issue.
> Maybe a solution would be to NOT use rlist for beta and for the PME
> potential, and instead to use rcoulomb or some extra variable... Then
> one could change the neighbor list (rlist) and rvdw without having to
> tweak the electrostatic interactions...
> > What is the optimal cut-off scheme is a different issue.
> > Indeed one would always want the force to go smoothly
> > at the cut-off, or before the cut-off in case one has charge groups
> > or nstlist>1.
> > However for PME one can not have 'exact' electrostatics while
> > the particle-particle force is zero at the cut-off since the reciprocal
> > space requires an error function contribution in real space.
> > Therefore the real space interaction has infinite range, but decays
> > very rapidly.
> > In PME the real space interaction is erfc(beta r)/r, which in Gromacs
> > is applied to all atom pairs in the neighborlist. The cut-off error
> > made here is very small, since ewald_rtol=1e-5 (I also often use 1e-6).
> > The alternative would be to somehow make the direct space interaction
> > go exactly to zero before the cut-off. This would lead to larger
> > errors, as one then misses more of the electrostatic interactions.
> > The only advantage would be that the integration could be more
> > reversible (assuming that all other algorithms are well reversible).
> >
> > Given the accuracies of all other algorithms I would say it does not
> > make sense to remove some electrostatic interactions at the cut-off
> > when they are already 1e-5 or 1-e6 smaller than the Coulomb
> > interaction at that distance.
> So, if I understand properly, you're saying that the notion of an
> electrostatics "cutoff" doesn't really make sense with PME, so my
> logic about having the neighborlist extend past the "cutoff" doesn't
> really apply. Rather, one just wants to ensure that the "cutoff" is
> sufficiently large that electrostatic interactions are fairly small
> and thus any inaccuracies due to neighbor list issues will be
> basically negligible...?
> Thanks,
> David
> > Berk.
> >
> >
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