AMBER: equilibration in explicit solvent

From: Amarda Shehu <>
Date: Sun, 4 Feb 2007 11:40:12 -0600 (CST)


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

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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Received on Wed Feb 07 2007 - 06:07:09 PST
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