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

JW Gibbs hanniballecter13 at gmail.com
Mon Jun 10 20:50:27 CEST 2013


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. 

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