[gmx-users] Clarity on TI free energy terms

[Nash, Anthony]

Dear Hannes,

Thanks for all the help yesterday, it helped. I, hopefully, have just the
one final question.

I am still a little confused how Gromacs deals with the interactions (vdW
& Coul) with the environment when a soft-core potential has been used to
switch between molecules (typeA and typeB in the topology file). I
understand how lambda can be used to 1) phase out the charge then 2) phase
out the vdW interactions for a molecule that is disappearing (or reverse
for appearing) to capture hydration energetics e.g., Justin¹s methane in
water FE tutorial. 

However, in the case of a D2K (aspartic-acid to lysine) dual-topology, how
are the vdW and charges brought back into play for typeB, when the
interactions of typeA have been coupled to lambda as per your example
below? 

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

I apologise if I may have misunderstood one of your earlier explanations,
I think this is the only piece of the puzzle left for me to understand.

Many thanks
Anthony



On 01/06/2016 19:04, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Hannes Loeffler"
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
Hannes.Loeffler at stfc.ac.uk> wrote:

>On Wed, 1 Jun 2016 16:15:31 +0000
>"Nash, Anthony" <a.nash at ucl.ac.uk> wrote:
>
>> In the mean while, do you know of any tutorials (besides the methane
>> in water FE tutorial) regarding TI for amino acid substitution?
>
>I am not aware of one.  You could try
>http://www.alchemistry.org/
>
>
>> And by ³q_off² and ³vdw_on/off², I assume you are referring to the
>> Œvalue¹ of the couple-lambda0: parameter?
>
>No.  I'm referring to the respective lambda paths.
>
>
>Cheers,
>Hannes.
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