[gmx-users] Re: Free Energy Calculations in Gromacs
jalemkul at vt.edu
Tue Jun 11 00:20:44 CEST 2013
On 6/10/13 2:50 PM, JW Gibbs wrote:
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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