[gmx-developers] ecomposition of Lennard-Jones contributions in free energy calculations with Gromacs

Berk Hess hess at kth.se
Fri Nov 11 18:34:52 CET 2016


I don't see how this would help FEP or TI. Decoupling Coulomb and LJ 
separately can provide more ensemble overlap in many cases. But 
decoupling repulsion and dispersion separately will always significantly 
decrease the ensemble overlap along the path, I would think.



On 11/11/2016 06:15 PM, Mark Abraham wrote:
> Hi,
> You can already do FEP from one atom type to another. So particularly 
> for combination rule 1 (see manual 5.3.2) you just choose V and W how 
> you want. But perhaps the special case also mentioned there does what 
> you want for the other combination rules.
> Mark
> On Fri, Nov 11, 2016 at 5:45 PM Joel Jose Montalvo Acosta 
> <montalvo161 at gmail.com <mailto:montalvo161 at gmail.com>> wrote:
>     Dear gromacs users and developers,
>     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 do this decouple independently?.
>     I know the great effort required to introduce this feature
>     directly in the source code (ie, writing, validating and
>     optimizing the new code), however, it will give a better control
>     of the FEP/TI simulations if we can do this decoupling from the
>     mdp input file. Thus, I invite to the gmx developers to include
>     this feature in the future gromacs releases.
>     Thank you,
>     Joel Montalvo
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