Re: AMBER: SANDER BOMB: volume of ucell too big

From: David A. Case <>
Date: Thu, 12 May 2005 13:27:50 -0700

On Thu, May 12, 2005, Stern, Julie wrote:

> It is a periodic simulation of alkylthiol chains. The sulfurs
> are restrained, but apparently did not stay in place. There is
> no solvent at all. I did look at the simulation (22 frames at
> .1 ps/frame was all I got). The volume expanded roughly 6 angstroms
> in both the x and y directions but hardly anything in the z-direction.

I'm assuming that you are trying to simulate a neat liquid of alkylthiol
chains (how long is the chain)? The results reported above suggest that your
initial density is way too high (hence the volume is expanding rapidly,
even over 2 ps.)

Amber is not well suited to simulations where the volume changes significantly
as a function of time: certain data structures are allocated based on the
initial structure, and are not updated correctly when the volume changes by a
large amount. Mike can probably suggest which variables to change to allow
bigger changes, but you could also try the following:

    Set taup=20.0 or so, and run a few picoseconds; then restart.
    Do this repeatedly until the volume equilibrates

This will slowly increase the unit cell volume, and the restarts will force
all of the data structures to be rebuilt. Be *sure* to visualize your
trajectories to be sure that the structures you get are meaningful. Unless
you have a good reason to restrain atom positions, it is best to avoid that.

.....good luck....dac

(note: if you are not trying to simulate a neat liquid, then you may be
heading in a wrong direction? Do you expect your system to have a
well-defined density at the given temperature and pressure?)
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Received on Thu May 12 2005 - 21:53:00 PDT
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