[gmx-users] FEP with bond formation, pair problem

[David van der Spoel]

Berk Hess wrote:
> Hi,
> 
> There are automatically different, since they are based on the A and B 
> state charges
> and the A and B state atom types.

But the problem is more complicated:

Let's say there is a Butane radical C4H9. that you want to bond to 
another butane radical to form octane (C8H18). Then the interactions 
that are non-bonded in the A state are excluded in the B state and 
replaced by pair interactions.

Is this supported in some way?



> 
> Berk
> 
>  > Date: Thu, 19 Nov 2009 16:15:52 +0100
>  > From: jochen at xray.bmc.uu.se
>  > To: gmx-users at gromacs.org
>  > Subject: [gmx-users] FEP with bond formation, pair problem
>  >
>  > Hi,
>  >
>  > how can I use different coulomb 1-4 interactions in the A and B state.
>  > The Manual just says
>  >
>  > [ pairs ] : LJ and Coulomb 1-4 interactions
>  >
>  > but, I far as I could see, did not give an example how the coulomb 1-4
>  > interaction can be explicitly given.
>  >
>  > Thanks a lot for any help,
>  >
>  > Jochen
>  >
>  >
>  > --
>  > ---------------------------------------------------
>  > Dr. Jochen Hub
>  > Molecular Biophysics group
>  > Dept. of Cell & Molecular Biology
>  > Uppsala University. Box 596, 75124 Uppsala, Sweden.
>  > Phone: +46-18-4714451 Fax: +46-18-511755
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se