[gmx-users] TI, sampling, sc_power, and sc_alpha

David Mobley dmobley at gmail.com
Mon May 29 17:28:22 CEST 2006

My take is that it is preferable to partition your vdW and charge
changes into two separate calculations, as the soft core settings that
work well for the vdW portion make the charging portion a more
"difficult" transformation than normal, and the settings that work
well for charging make the vdW portion "difficult". In my experience,
I can get by with fewer lambda values by doing  the calculation in two
portions than I would need to do it all together.

Also, I find that the parameters which work best for vdW are alpha=0.5
and sc-power=1, which is what Michael Shirts had come up with as close
to optimal. When I deviate from those, the dv/dlambda curve gets a lot
less smooth and I get much larger errors -- especially if I go up
above alpha=1 (and even more so at alpha=2).

If I were you, I would probably set up a test calculation where you
are only changing vdW interactions, and then play a bit with the alpha
(and lambda spacing) to see what gives you the smoothest dv/dlambda
curve for which you need the fewest lambda values. Then you can add
back in the charge modification, if you like, and see if this messes
up the curve a lot. If so, then do the charges in a separate
calculation before/after changing the vdW (depending on what exactly
you're doing with the charges).


On 5/29/06, Berk Hess <gmx3 at hotmail.com> wrote:
> >From: mernst at tricity.wsu.edu
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: gmx-users at gromacs.org
> >Subject: [gmx-users] TI, sampling, sc_power, and sc_alpha
> >Date: Fri, 26 May 2006 12:36:20 -0700 (PDT)
> >
> >Greetings once again fellow Gromacs-users,
> >
> >I have seen a substantial and disturbing change in calculated free energy
> >differences
> >between systems run with Gromacs 3.3 and Gromacs 3.3.1. I am trying to
> >determine if
> >these differences are due to the new software, new parameters, insufficient
> >sampling, or
> >something else, and I don't have enough computer time to investigate every
> >possible
> >combination. I turn to the list for insight.
> I had implemented the alpha=1 option in 3.3 and set it as default,
> since it seemed to produce "better" dH/dl curves, especially for LJ-only
> perturbations.
> Only some time after the 3.3 release I realized that this might cause a lot
> of trouble as people probably did not realize that the default alpha value
> had changed. I apologize for having caused such inconveniences.
> To prevent such mistakes I have set default value to zero in 3.3.1,
> which is not allowed, so people are forced to think about alpha.
> The problem is that there is not (yet) an optimal soft-core dependence
> for combined charge/LJ perturbations. For LJ only alpha=1 is quite optimal.
> But for charge perturbations alpha=1 causes an extremely sharp peak
> exactly at lambda=0 (or 1). For alpha=2 this peak at zero shift to values
> slighlty
> above zero and becomes less sharp, here you have to sample the both slopes
> of the peak.
> With alpha=1 you need a very non-linear lambda distribution with a very
> fine spacing close to 0. With alpha=2 you also need a fine spacing at 0,
> but probably also in the middle where the particles start overlapping.
> I would guess that especially alpha=1 can give an enourmous error
> if you only used 21 evenly spaced points. Adding points at 0.01 and 0.02
> from lambda=0 and/or 1 could help a lot.
> Berk.
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