Re: AMBER: Using TLEAP to set up MD in the crystal lattice space?

From: Thomas Cheatham <>
Date: Mon, 13 Aug 2007 20:45:19 -0600 (Mountain Daylight Time)

> > how to solvate this system, but I think the best strategy would be to hold
> > the protein with tight restraints for successive additions of water
> > molecules and simulation in the NVT ensemble, then simulation in the NPT
> > ensemble while maintaining the protein atom restraints as small numbers of
> > water molecules are added or taken away until the pressure stabilizes at
> > 1atm with the right unit cell volume.
> You are right that figuring out how many waters to add, and where they should
> go, is a challenging task. You need to try to get the starting configuration
> as good as possible, since the time required to relax waters from "bad"
> positions to good ones might be prohibitively long. You might look at packmol

A couple of papers by Darden and co-workers (one is Bevan et al in BJ in
~2000) used constant pressure equilibration of the full crystal to find
the correct number of waters. Also, beyond packmol, you could try Mezei's
software simulaid (

-- tom

p.s. I do not think CHARMM has any special way of doing this, re:
equilibration of solvent/ions in a crystal lattice.
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Received on Wed Aug 15 2007 - 06:07:37 PDT
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