[gmx-users] Re: Free Energy Calculations in Gromacs

[Justin Lemkul]

On 6/10/13 2:50 PM, JW Gibbs wrote:
> Hi,
>
> I have been trying to perform the simulations using the amber forcefield, in
> which the [ pairtypes ] directive is not defined explicitly in the
> ffnonbonded.itp file, but rather the 1-4 interactions are generated as per
> the defaults section in the forcefield.itp file. I was wondering what
> happens to these 1-4 interactions at lambda=1 state?
>
> Suppose 1 corresponds to CA and 4 corresponds to NA at state A (lambda = 0)
> and the CA_per and NA_per are the corresponding atomtypes at state B (lambda
> = 1).
>
> It is defined in the topology file that
>
> ...
> ...
> [ pairs ]
>
> 1      4       1
> ....
> ....
>
> So does it mean that at state B (lambda = 1), the 1-4 nonbonded interactions
> will be calculated between CA_per and  NA_per?
>
> Although the [ pairs_nb ] section is described in the manual, I would
> appreciate if someone elaborates a little more.
>

The actual answer depends on exactly how you're treating the system.  Are you 
using [pairs_nb] in your topology or just [pairs]?  The outcome will be 
different depending on which you're using.  Also note that, as the manual says, 
you don't really need to mess with [pairs_nb] at all; you can achieve unscaled 
internal interactions using "couple-intramol = no" in the .mdp file.  Without 
seeing the .mdp file, it's even more difficult to know what you're doing and 
what you should expect.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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