AMBER Archive (2009)


From: David A. Case (
Date: Thu May 28 2009 - 09:29:50 CDT

On Wed, May 27, 2009, PRADEEP VENKATARAMAN wrote:
> I am trying to do a NPT simulation on 300 methane molecules in 25 X 25 X 25
> box at 1 atm and 300 K.
> So initial density is 0.768 g/cc which is closer to actual density of
> methane gas.

??? are you sure?

> Since there is no solvent, the volume is expected to increase very rapidly.
> Hence I use taup=20.0 and dt =0.002.

Sander is designed for condensed phase simulations. It will crash when there
are rapid changes in volume, as you have here, and all kinds of things are
non-optimal for gaseous simulation.

You can try to restart (as the message suggests), but you may need to either
move to a fixed volume simulation or find another program. The barostat in
sander has never been tested on gases, so it's not even guaranteed to give the
correct density (which will be *very* low, I think).

Finally, what do you hope to learn here? At 300K and 1 atm., methane is very
close to an ideal gas...I'm not sure that you could get good enough statistics
to identify any deviations from ideality. Of course, if this is just a
learning experience, go for it -- you're sure to learn interesting things
about how simulations work or don't work.


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