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

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Wed, 2 Jun 2010 14:26:43 -0700

> The purpose of my dynamics is checking the sugar solubility in ionic liquid
> by various method.
> Ionic liquid has poor sugar solubility. But when I use water-mediated
> method(mentioned previous mail), sugar solubility in ionic liquid has been
> increased. This method has proven to be useful by real experiment. So I'd
> like to know why solubility has been increased when using water
> mediated-method by MD
> Are there any method to mimic this procedure?

The best way is the vacuum method I gave. The waters that
evaporate (as well as any other molecules) will remain in
the simulation, but distance will weaken the interactions
with the remaining mass. Whether the process of evaporation
(if successful) would tell you about sugar solubility is
an interesting question; I would read up on how accurate
such simulations are with e.g. TIP3 force field. It sounds
like an interesting thing to try for ideas anyway.

> How about "Strip" command in PTRAJ? Does it affect the sugar molecules like
> real evaporation?

No, it just makes them disappear from the output of the simulation.
Then you would have to set up another simulation with the remaining
coordinates and equilibrate it etc.


> Thank you as always

> Regards,

> Hoshin Kim.

> ----------------------------------------------------------------------------
> -------
> Hoshin Kim
> Now)
> Visiting Scholar
> Department of Chemical and Biomolecular Engineering
> North Carolina State University
> Raleigh, NC 27695
> Phone: 919-986-9258
> Also)
> Graduate student (M.D. candidate)
> Ionic Liquids Team(ILs) in Bio Nano Process Lab
> Department of Biological Engineering,
> 2S 113, Engineering building Inha University,
> 253 Yonghyeon Dong, Nam Ku
> Incheon, KOREA
> TEL) +82-32-860-8655
> ----------------------------------------------------------------------------
> -------

> -----Original Message-----
> From: [] On Behalf
> Of Bill Ross
> Sent: Thursday, June 03, 2010 4:54 AM
> To:
> Subject: Re: [AMBER] Is it possible to revome water molecules during
> simulation?

> > 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.

> Bill

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Received on Wed Jun 02 2010 - 14:30:03 PDT
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