[gmx-users] Question about Justin's Free Energy Tutorial

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 6 20:42:35 CEST 2011

Fabian Casteblanco wrote:
> Hello Justin,
> I have a question about your tutorial.  If I want to mutate one small
> group of a molecule, I would have to not provide 'couple_lambda0' and
> 'couple_lambda1', correct?  I would essentially have to follow sec
> 5.7.4 in the Gromacs manual and I have to actually provide all state A
> variable and all state B variables.  Gromacs would calculate the new B
> state parameters for bond lengths, angles, etc, correct?  Are there
> any other major differences to account for?

I have never attempted FEP with the new free energy code.  Try a simple test 
system first and make sure it works as expected.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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