Re: [AMBER] Suggestion for minor user manual clarification

From: Carlos Simmerling <>
Date: Tue, 21 Jun 2011 14:22:47 -0400

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
not sure if that's what you meant...

On Tue, Jun 21, 2011 at 2:13 PM, Christoph Klein <> 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<>,
> 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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Received on Tue Jun 21 2011 - 11:30:04 PDT
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