RE: AMBER: equilibration in explicit solvent

From: Yong Duan <>
Date: Sun, 4 Feb 2007 11:07:30 -0800

As Dave said, this may not be a productive approach if you intend to use it
to assess the stability of the conformations (energy fluctuation is
proportional to sqrt(N), N is the number of atoms). You'd likely have to run
VERY long simulations to ensure a reliable result. More importantly, such
comparison is fundamentally flawed without the consideration of entropy.

If the two systems are identical (same protein and same # of ions) and the
only difference is between the conformations, you can construct two systems
which, as you noted, will have different # of water. You can then mannually
edit the larger of the two systems to remove those "excessive" water
molecules. This can be easily achieved by editing the coordinate file
generated from x/tleap since the water molecules are at the "end" of the
file. You can compare the size of the coordinate files and remove the
"excessive" entries in the larger one. After the editing, you can use the
topology file of the smaller system for the edited system after updating the
box information.

Good luck!


-----Original Message-----
From: [] On Behalf Of
Amarda Shehu
Sent: Sunday, February 04, 2007 9:40 AM
Subject: AMBER: equilibration in explicit solvent


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 - 06:07:11 PST
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