Re: [AMBER] Is it possible to revome water molecules during simulation?

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Wed, 2 Jun 2010 12:53:48 -0700

> I'm trying to do molecular dynamics of sugar solvation in ionic liquids.

> The solvation procedure is below,
> First, sugar were added into water, and then this mixture(sugar + water)
> were added into ionic liquid solvent.
> Removing the water molecule by using Vacuum evaporator at 60'C.
> Now I made solvent box mixed with sugar and water, and ionic liquid solvent
> box.(their equilibration and production run(4.5ns) were already finished)
> Then I put the water + sugar mixture into ionic liquid. But I can't make
> progress, because I don't know how to remove water molecule during
> production run.
> So, question is "Is it possible to remove water molecule during simulation?"

No. Probably what you need to do is run a separate simulation
without water. An alternative would be to run without a periodic
boundary (vacuum) and see if the waters 'evaporate' into the void.

It might help if you state what you are trying to learn.


AMBER mailing list
Received on Wed Jun 02 2010 - 13:00:04 PDT
Custom Search