[gmx-users] soft-core potential in combination with PME

David Mobley dmobley at gmail.com
Thu Apr 19 21:01:13 CEST 2007


> Tanks for your elaboration on the subject. I've done a couple of free
> energy simulations myself, also on disappearing charged atoms, but so
> far I've not yet encountered any of the instability problems you
> mention here (though I did encounter instabilities at high lamda
> values, caused by the flying ice cube problem). Your problem could
> very well be related to the force field, since I'm using G53a6 and
> you're probably using OPLS. Maybe the extra hydrogens are causing
> your troubles?

I recommend Langevin dynamics (sd) to avoid the flying ice cube and
related nonergodicity problems.

I'm using AMBER. Yes, there are extra hydrogens. Related? Not sure.

> I agree with you that the ideal soft-core parameters for decoupling
> LJ may not be so ideal for decoupling Coulomb, and that this can lead
> to convergence problems and wrong free energy results. In that case a
> separate decoupling of LJ and Coulomb forces in fact may be the best
> answer.


> Btw, David, are you still interested in feedback on your free energy
> tutorial, or do you consider that project finished? I used it as a
> starting point for my simulations and may have some interesting
> remarks and/or suggestions.

It's not done; I need to do a much more extensive one at some point. I
just put it up as a crude starting point. But feel free to send me
comments off list if you have anything to say in terms of
clarifications of the current one: I will be expanding it eventually,
but in the meantime I can fix errors in the existing one or clarify.


> Greetings,
> Jeroen
> > Date: Fri, 13 Apr 2007 09:18:21 -0700
> > From: "David Mobley" <dmobley at gmail.com>
> > Subject: Re: [gmx-users] soft-core potential in combination with PME
> >       (sorry, again)
> > To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > Message-ID:
> >       <bc2c99750704130918j7e8add8ene9df87cb93bb19be at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Berk and all,
> >
> > > I don't understand what David Mobley meant exactly.
> > > There is no Coulomb singularity with soft-core.
> > > Maybe one could have an unfortunate situation where the LJ
> > > is already very soft, but the Coulomb not very soft,
> > > which could lead to instabilities.
> > > But I have never encountered this.
> >
> > Anytime I do a simulation where I turn of both coulomb and LJ
> > interactions at the same time, I run into this problem. Sometimes it's
> > worse than others. Maybe it's because the 1/r^12 and 1/r have
> > different r-dependencies? I don't know.
> >
> > I suspect the issue partly is just what's optimal: The soft core
> > parameters that would be optimal for modifying Coulomb interactions
> > are not optimal for modifying LJ interactions, and vise versa. So if
> > you use soft core settings that give you a smooth transformation for
> > LJ interactions, you do too  much or too little smoothing of the
> > Coulomb interactions and introduce large Coulombic forces. On the
> > other hand, if you pick soft core parameters that are good for Coulomb
> > interactions, you end up with large LJ forces. (For example, Coulomb
> > transformations are nearly optimal with LINEAR lambda scaling
> > (sc-alpha=0), but that doesn't work *at all* for LJ transformations.
> >
> > If I remember correctly, basically what the Anwar paper tries to
> > achieve is separately smoothing the two. You could probably accomplish
> > the same thing by allowing separate sc-alpha and sc-power for Coulomb
> > and LJ interactions so they can be tuned separately.
> >
> >
> > So, while formally using soft core for Coulomb removes the
> > singularity, in practice I think the forces are still large enough
> > (when using soft core parameters are tuned for LJ interactions) that
> > instabilities result (at least for the stuff I do, with the force
> > field I use). Hence my recommendation to do two stages.
> >
> > Anecdotally, I should mention that a bunch of different people have
> > e-mailed asking me about various problems they're having where they
> > get unexpected free energies, etc. I suggest they do the Coulombic and
> > LJ parts separately, and invariably they write back that it works much
> > better.
> >
> > David
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