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

[Jochen Hub]

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: 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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>


-- 
---------------------------------------------------
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
---------------------------------------------------