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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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