[gmx-users] Treating solute as a rigid body with flexible solvent molecules

Mark Abraham Mark.Abraham at anu.edu.au
Thu May 10 12:27:29 CEST 2012

On 10/05/2012 7:29 PM, Debayan Chakraborty wrote:
> Dear Gromacs Users,
>                                   I want to simulate an organic dye in 
> a solvent ( such as aniline as DMA). I have already relaxed the 
> solvent around the dye  in the equilibration run ( NPT) using position 
> restraints on the solute. Now for the production run I want to release 
> the position restraints on the dye and allow it to translate and 
> rotate like a rigid body under the influence of the solvent. I am  new 
> to GROMACS, and I am not sure what is the best way to realise this. 
> Any help would be greatly appreciated.

This kind of procedure is done in lots of simulations - have a look at 
some tutorial material and you should learn how to do this, and a lot 
more besides!


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