Re: [AMBER] Solvation in water

From: Jason Swails <>
Date: Fri, 2 Jul 2010 11:57:37 -0400

This sounds like an imaging problem. The problem is that only one periodic
image has its coordinates saved to the trajectory file. Therefore, you're
visualizing water molecules from a bunch of different boxes as some water
molecules diffuse out of the current box. In the simulation, each other
water molecule is still there in terms of force calculations, but they're
not written to the trajectory file so you can see them.

You can use the variable iwrap=1 in sander/pmemd input file to wrap
molecules leaving the box into the other side. This is discussed to a great
extent here on the list. You can also use the center and image commands in
ptraj to accomplish the same thing.

Hope this helps,

On Thu, Jul 1, 2010 at 10:39 PM, Hoshin Kim <> wrote:

> Dear amber user,
> I'm trying to do sugar solvation simulation in water(liquid state). I want
> to know that my result of simulation has been solvated in liquid water.
> Because the distance between water molecules are too far to calculate
> h-bond
> energy. It means water molecules were scattered like gas state.
> I did equilibration in NVT/NPT at 300K. and density is correct(almost
> 1.00).
> production run has been carried out for 4.5ns at 300K (NPT).
> Attached herewith is result PDB file. Please check this file and tell me
> whether that sugars are in liquid sate water. If it is not liquid state,
> how
> can I do solvation simulation in liquid state water box?
> Thank you in advance.
> (8-glucose molecules are put into TIP3PBOX which was used as water box.)
> 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
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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Jul 02 2010 - 09:00:06 PDT
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