Re: ABF tutorial; updated FEP tutorial

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Fri Mar 21 2008 - 18:53:58 CDT

Hi Lei,
The expression for the size correction in the text is in reduced units
- for more clarity the denominator should have an additional factor of
4 pi epsilon_0. Also, q_0 is 0 and q_1 is the elementary charge e
(they are swapped in the text, plus the reduced unit thing).
A very similar expression is given in more detail there:
http://en.wikipedia.org/wiki/Madelung_constant

Working out a few unit conversions, one ends up with -16.2 kcal/mol.
Here is what the complete numerical calculation looks like once you
simplify the powers of ten:
-.5 * 2.837 * 1.602^2 * 6.022 * 10^5 / (1.112 * 29.1) / 4184

I hope it clarifies the problems with this section.
Jerome

2008/3/20 Lei Shi <les2007_at_gmail.com>:
> Hi, Jerome
>
> On page 15 of the alchemical FEP tutorial,
> "A periodic cell length of L = 29.1A yields a size-dependence correction of
> −16.2 kcal/mol"
> Can you show more details on how you get the "-16.2" value?
>
> In addition, in Table 4 of Grossfield et. al. (JACS 2003 125:15671-82),
> there are a few values for Na solvation, is the "-91.0" there for charmm27
> comparable to your -94 or -110.2?
>
> Thanks.
> Lei
>
>
>
> On Thu, Mar 20, 2008 at 4:55 PM, Jerome Henin <jhenin_at_cmm.chem.upenn.edu>
> wrote:
>
> > Dear NAMD users,
> > We are happy to announce a brand-new ABF tutorial - an occasion for
> > the curious among you to get acquainted with the method, working on
> > three simple cases that should let you have the fun without too much
> > of the pain:
> > http://www.ks.uiuc.edu/Research/namd/tutorial/abf/
> >
> > The alchemical FEP tutorial has also been updated, including a new
> > exercise about a purely electrostatic perturbation, to see a slightly
> > different kind of physics at play:
> > http://www.ks.uiuc.edu/Research/namd/tutorial/fep/
> >
> > Check them out, and let us know if you have comments!
> >
> > Jerome Henin and Chris Chipot
> >
> >
>
>
>

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