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

From: Hoshin Kim <85hskim.gmail.com>
Date: Thu, 3 Jun 2010 15:40:11 +0900

Dear Amber user,

First of all, I'm the beginner of Amber and molecular dynamics.

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?"

Thanks you in advance,


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

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Received on Wed Jun 02 2010 - 13:00:03 PDT
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