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!
Mark
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