Right. Sorry I didn't articulate my point quite as clearly as intended.
The manual specifies that the parameters of the paper were used for igb=1.
Some readers might think that the offset was one of those parameters from
the paper, so that when using igb=1, the default value of the offset is
0.13.
I know I did! Instead, for igb=1, it might be best to say in the manual
that
to replicate the results of the referenced paper, they should manually set
offset = 0.13, instead of using the default 0.09.
On Tue, Jun 21, 2011 at 2:22 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> the offset value is specified separately in the input and isn't part
> of the igb=1 specific code. it's up to the user to decide the offset
> value.
> not sure if that's what you meant...
>
>
> On Tue, Jun 21, 2011 at 2:13 PM, Christoph Klein <ctk3b.virginia.edu>
> wrote:
> > Hello all,
> >
> > I was trying to implement a replica of the GB model corresponding to
> igb=1
> > (HCT with modifications by Tsui & Case). I was able to do so but got hung
> up
> > on the parameterization for a bit.
> >
> > In the user manual it is stated that igb=1 is implemented "with
> parameters
> > described by Tsui and Case". In the relevant
> > paper<http://www.ncbi.nlm.nih.gov/pubmed/11754341>,
> > the offset parameter, with a default value of 0.09A, is adjusted to
> 0.13A.
> > However, as near as I can tell, the actual implementation corresponding
> to
> > igb=1 retains the default value of 0.09A. If this is indeed the case, I
> feel
> > this might be a distinction worth making in the manual.
> >
> > Best,
> > Christoph Klein
> > _______________________________________________
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> >
>
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--
Christoph Klein
University of Virginia
B.S. Chemical Engineering
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Received on Tue Jun 21 2011 - 13:00:05 PDT
