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

Michael Shirts mrshirts at gmail.com
Fri Oct 7 16:24:07 CEST 2011

I don't think this is a question about new free energy code -- I think
this is asking about the fact if you can do a free energy calculation
by specifying the A and B variables in the topology, instead of using
the MDP coupl-moltype arguments.  This is actually the way free energy
calculations were managed before 4.0, and is still supported.

The answer is yes, though it requires some experience with what's
going on -- and I don't have time to document it all quite right now,
as it's described relatively thoroughly in the manual.

The one difference is that the coupl-moltype keywords makes it easy to
decouple molecules (turn off the intermolecular but not intramolecular
energies) from their environment, which is very hard (and sometimes
impossible) to do by changing A and B states. If you want to turn off
all interactions, then you can do it very straightforwardly by
changing the top files.


On Thu, Oct 6, 2011 at 2:42 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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
> 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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