Re: AMBER: equilibration in explicit solvent

From: Amarda Shehu <>
Date: Sun, 4 Feb 2007 12:32:05 -0600 (CST)

I see. So it will involve playing around with the dimensions to ensure the
same number of water molecules.

These two conformations have been obtained with a newly developed method
in implicit solvent (using ff03 and GB). I am preparing a manuscript for
publication, but my advisor has asked me to make sure that in explicit
solvent, these conformations retain both their structural integrity and
their energetic difference.

With the NVT equilibration (same dimension for boxes -- about 214 water
molecules difference), I have been able to see that the structures at the
end of the equilibration remain very similar (0.5 A all-atom least RMSD)
to the structures at the beginning of the equilibration. I made sure the
equilibrations were rather long.

The problem is that the final energies between the two structures are in
the order of thousand of kcal/mol. The initial conformations, in implicit
solvent, differ from each-other in less than 0.5 kcal/mol. After the
equilibration, the difference is rather large. Most of this may be
attributed to the difference of 214 water molecules.

I am not sure whether simply counting out the water contribution (which I
do not know how to do either) and reporting the energy difference between
the two conformations without the water molecules is enough. I was told to
seek an equilibration that from the start would have the same number of
water molecules and the same density at the end.


On Sun, 4 Feb 2007, David A. Case wrote:

> 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.
> ...regards...dac
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to
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