David van der Spoel wrote:
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?
Actually for the LJ part that is supported. The solution is to turn the
normal non-bonded LJ in part A into pairs and explicitly give the
standart sigma/epsion as A, and zero sigma/epsilon (for 1-2 and 1-3 in
B), or scaled (for 1-4 in B) as B state parameters.
So far so good. But can the same be done for the colomb 1-4 interactions
in the B state? The problem arises since the 1-4 coulomb interactions
are scaled down by 1.2 in the AMBER FF, so I need different 1-4 coulomb
interactions in A and B.
In principle that problem should be in any FEP calculation which
includes the formation of a bond.
Jochen
Berk
> Date: Thu, 19 Nov 2009 16:15:52 +0100
> From: [email protected]
> To: [email protected]
> 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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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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