[gmx-users] soft-core and coulomb transformation

[Berk Hess]

Hi,

The bug was indeed was I expected.
I have fixed it for version 3.3.3.

You might not notice it easily, since the direct space contribution is 
usually
larger than the mesh part.
But for a two particle system I got nan's.

Berk.


>From: "David Mobley" <dmobley at gmail.com>
>Reply-To: 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] soft-core and coulomb transformation
>Date: Mon, 12 Nov 2007 16:17:36 -0800
>
>Berk,
>
> > But what do you mean with charging and discharging?
> >
> > Going one way or the other in lambda does not matter.
> > What matters is if there are particles that have zero charge
> > in the A-state topology, while they have a non-zero charge
> > in the B-state topology.
>
>Sorry, what I mean by "charging" versus "discharging" is that
>"charging" is where the A state has zero charges and the B state has
>normal charges, and discharging is the reverse. So "charging" is the
>scenario you describe, and "discharging" is the reverse.
>
>David
>
> > Berk.
> >
> >
> > >From: "David Mobley" <dmobley at gmail.com>
> > >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > >To: "bharat v. adkar" <bharat at sscu.iisc.ernet.in>
> > >CC: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > >Subject: Re: [gmx-users] soft-core and coulomb transformation
> > >Date: Mon, 12 Nov 2007 10:26:37 -0800
> > >
> > >Following up on this issue, discharging phenol in water appears to
> > >give the same results as charging phenol in water. In other words, so
> > >far the only cases for which there seem to be a problem are relative
> > >calculations (and so far I haven't looked at this for any other than
> > >Bharat's test cases).
> > >
> > >Bharat, be sure you submit a bugzilla and we'll see how things go from
> > >there. I may at some point try setting up some of my own relative free
> > >energy topologies and see if I see the same effects, but I'm not
> > >likely to have time for that for a couple days.
> > >
> > >Thanks,
> > >David
> > >
> > >
> > >
> >
> >
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