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

From: Hoshin Kim <>
Date: Thu, 3 Jun 2010 16:59:27 +0900

Dear Bill and Amber user

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

Thank you as always


Hoshin Kim.

                   Hoshin Kim
Visiting Scholar
Department of Chemical and Biomolecular Engineering
North Carolina State University
Raleigh, NC 27695
Phone: 919-986-9258
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
Subject: Re: [AMBER] Is it possible to revome water molecules during

> 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

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.


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Received on Wed Jun 02 2010 - 14:00:04 PDT
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