Re: AMBER: equilibration in explicit solvent

From: Ilyas Yildirim <>
Date: Mon, 5 Feb 2007 00:13:48 -0500 (EST)

Hi Amarda,

I had the same problem before. I have written a perl script which does the
following: You create the first .pdb file with water molecules in it. You
create the other .pdb file, which needs to have more water molecules in it.
Then, using this script, it will make sure that the 2nd .pdb has the same
number of water molecules as the 1st one. Note here that deleting the
water molecules by hand is not the best way; the reason is, it will delete
the water molecules in one region in the box, which will be a problem when
equilibrating the system. With this perl script, it will keep the water
molecules close to the center of the box (assuming the solute is centered
around the origin).

If you are still interested, I can send the script to you.


On Sun, 4 Feb 2007, Amarda Shehu wrote:

> Hello,
> I am trying to equilibrate in explicit water two conformations of the same
> system, separately. I followed some amber tutorials on how to add a water
> box and how to carry out an NVT equilibration. The problem is that a box
> of the same dimensions produces a different number of water molecules in
> each case. The difference is around 200 water molecules.
> Since I want to compare the final energies of the conformations after the
> equilibration, I want to maintain the same number of water molecules in
> each box. Is there a way to do this from the start? I have tried playing
> with different box dimensions for each of the systems but this is a very
> difficult hit-and-miss. I cannot find anywhere in the manual a way to do
> this.
> In addition, I want to run an NPT equilibration after the NVT one. Can one
> point me to a tutorial on how to do so? I have to make sure that the
> densities at the end of the simulations are the same and that there are no
> bubbles of air in my solvent boxes.
> Any help will be greatly appreciated. I have perused through the amber
> e-mails but have not been able to find a lead.
> ***********************************
> Amarda Shehu,
> Graduate Student, Computer Science,
> Rice University.
> ***********************************
> -----------------------------------------------------------------------
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  Ilyas Yildirim
  - Department of Chemisty       -				-
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Received on Wed Feb 07 2007 - 06:07:15 PST
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