[gmx-users] Clarity on TI free energy terms

[Hannes Loeffler]

On Wed, 1 Jun 2016 12:06:20 +0000
"Nash, Anthony" <a.nash at ucl.ac.uk> wrote:

> vdw_lambdas              = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35
> 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
> mass_lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
> 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
> fep_lambdas =  0.0 0.1 0.1 0.2 0.2 0.3 0.3 0.4 0.4 0.5 0.5 0.6 0.6
> 0.7 0.7 0.8 0.8 0.9 0.9 1.0 1.0

This will transform both vdW _and_ Coulomb terms at the same time but
at a different pace.  Maybe you want something like

fep-lambdas = 0.0 0.2 0.4 0.6 0.8 1.0  1.0  1.0  etc.
vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0  0.05 0.10 etc.
mass-lambdas as above

This will first transform Coulomb and bonded terms in the first six
lambdas and vdW from the 7th lambda onwards.  This also assumes that
you have vanishing atoms only.  If you have appearing atoms only you
would obviously have to revers the order, and when you have both you
will have to run with two mdp/tpr setups.


> couple-moltype           = protein
> couple-lambda0           = vdw-q
> couple-lambda1           = vdw-q

This will decouple all atoms in the 'protein' selection from the
environment.  This is for absolute transformation and not what you seem
to want to do i.e. a relative transformation of one residue into
another.  So avoid those parameters.