[gmx-users] disabling nonbonded interactions between two specific groups

Dallas Warren dallas.warren at monash.edu
Thu Apr 11 01:04:21 CEST 2019

I imagine you could do the first by having the two groups represented by
duplicated atom types (you'd have to create them in the FF files), then
turn off the interactions between them using normal lamba methods, but
leaving all the other interactions untouched.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a

On Thu, 11 Apr 2019 at 08:33, Irem Altan <irem.altan at duke.edu> wrote:

> Hi all,
> Is it possible to disable nonbonded interactions between two specific
> groups? What I would like to do is a type of alchemical transformation to
> calculate free energies. Are  the following steps possible within Gromacs?
> - to have a molecule represented with standard force fields AND a Lennard
> Jones particle superimposed on it
> - the molecules interact with each other and the LJ particles interact
> with each other but the molecules don’t interact with LJ particles
> - across multiple simulations, the interaction energy of one species gets
> turned off gradually
> For the last part, is it possible to weaken the bonded interactions of the
> molecules and not have them fall apart by restraining the bond lengths with
> lincs? If so, can something similar be done to the dihedrals?
> Best,
> Irem
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