[gmx-users] free energies with tabulated potentials or PME

Berk Hess gmx3 at hotmail.com
Tue Oct 31 10:41:53 CET 2006

>From: Michael Brunsteiner <mbx0009 at yahoo.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx users <gmx-users at gromacs.org>
>Subject: [gmx-users] free energies with tabulated potentials or PME
>Date: Mon, 30 Oct 2006 14:56:10 -0800 (PST)
>hi everybody,
>Can somebody tell me whether free energy calcs (TI)
>can be done in combination with user defined tabulated
>potentials ? ... or in other words: is dU/dlamda
>calculated numerically or analytically ?

This is not a question of numerical vs analytical.
dU/dlambda = dU_B - dU_A.
This only means you need to evaluate the energy twice
with a different set of parameters.
Free-energy as well as soft-core interactions are implemented
for all possible combinations.

>I understand that in gmx-3.3.1 free energy + PME is
>supported, has anybody tested this implementation in
>terms of accuracy/speed ?

I have implemented that and it is only slightly slower
than without free energy.
I do not understand your question about accuracy.
There are no approximations, so it is fully accurate.


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