[gmx-users] Question about decomposition of Lennard-Jones contributions in free energy calculations with Gromacs

David van der Spoel spoel at xray.bmc.uu.se
Mon Nov 7 16:16:40 CET 2016

On 07/11/16 15:55, Joel Jose Montalvo Acosta wrote:
> Dear Dr. van der Spoel,
> My name is Joel Montalvo, I'm a PhD student computational chemistry in 
> the University of Strasbourg (France). I'm interested in computing 
> solvation free energy of solutes with apolar character as fullerenes 
> and graphene in organic solvents, using free energy perturbation (FEP) 
> and thermodynamic integration (TI) techniques as implemented in gromacs.
> I write because I would like to decouple independently the dispersion 
> and repulsion components of the Lennard-Jones term in a FEP/TI run 
> such as it happens with electrostatics and Lennard-Jones interactions. 
> How can I modify the gromacs source code in order to make this 
> decouple independenly?. I image that in the mdp input file, the 
> options couple-lambda0 and couple-lambda1 could accept new values as 
> "disp" for dispersion and "rep" for repulsion. Also, it is possible to 
> have new lambda-vector sections, "disp-lambdas" and "rep-lambdas" for 
> controlling independently both contributions during a FEP/TI run.
> I find interesting this decomposition because, first, the convergence 
> profiles for both contributions are different, so I could use a 
> different number of lambda for dispersion than for repulsion, similar 
> to what happens with electrostatics and Lennard-Jones contributions. 
> Second, it will be valuable to have the dispersion/repulsion 
> contribution ratio for solvation free energies of different solutes.
> Thank you in advances for any comment or help
> Joel Montalvo Acosta
This is a regular gromacs question so please continue the discussion on 
the gromacs user list.
I think you can simply define A and B values for C6 and C12 in your 
topology file and the do the TI in multiple steps. You will have to turn 
off the C6 first I guess, since the goes to -infinity. However, then I 
don't see how you could ever get converged values for the next step, 
since then you are left with a completely repulsive potential (it might 
work in NVT though).

However before you even start you should ask yourself what it means. 
Will you get any meaningful results? Decomposing in enthalpy and entropy 
is meaningful, but energy components is not.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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