[gmx-users] particle transfer molecular dynamics

Mark Abraham Mark.Abraham at anu.edu.au
Sat Jan 28 23:43:19 CET 2006

> I want two boxes to be coupled together at T,P. one box will have water and the
> other polymer and water. Do molecular dynamics in this two boxes until the
> chemical potential of one box is equal to the chemical potential of the other
> (in other words, to have phase equilibrium). In order to achieve that solvent
> molecules must be transferred to the other box during the MD simulation . 
> is that feasible in Gromacs?

You will run into all kinds of problems transferring molecules to the 
other box. First you need a big enough hole to insert them in, and then 
you'll need to re-equilibrate both boxes - I suspect this would take 
longer with the boxes coupled than with a box coupled to a thermal sink. 
In any case, in gromacs you can couple a box to a thermal sink, but not 
to another box - though perhaps that would be possible with some source 
code hacking.


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