You can strip water residues out of a coordinate file using ptraj, but you
will have to create a new topology file that has the appropriate number of
water molecules (0 if you strip them all).
See the "strip" command in the ambertools manual (under ptraj), and the
syntax of the amber mask.
There's no way of removing the water during the course of the simulation
(except for TI, but that doesn't appear to be what you're trying to do).
Good luck!
Jason
On Thu, Jun 3, 2010 at 2:40 AM, Hoshin Kim <85hskim.gmail.com> wrote:
> 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,
>
> 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
>
> ----------------------------------------------------------------------------
> -------
>
>
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Jun 02 2010 - 13:00:05 PDT
