Re: AMBER: equilibration in explicit solvent

From: David A. Case <>
Date: Sun, 4 Feb 2007 10:21:18 -0800

On Sun, Feb 04, 2007, Amarda Shehu wrote:
> 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,

This is likely to be a disappointing exercise, since fluctuations in the
(potential) energy will be large, and differences in the averages are difficult
to interpret in any event. What is it that you really want to estimate?

> 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.

Hit and miss might be the easiest strategy. Once you get close, just create a
pdf file of the one with the slightly larger number of waters, and manually
delete a few. Then re-load the resulting pdb back into LEaP.

> 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

You can't do this: with different solvents, the equilibrium densities will be
probably not be exactly the same. See my first comment above.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Feb 07 2007 - 06:07:10 PST
Custom Search