Hi!
I'm new to MD and was hoping someone could help me with a query I had
regarding the amber tutorial:
TUTORIAL A9: Thermodynamic Integration using soft core
potentials<
http://ambermd.org/tutorials/advanced/tutorial9/index.html>
I have followed it through and got the results I was after, but was confused
about why the equilibration phase does not operate under constant volume as
is suggested in the amber 10 manual.
"If NTB .NE. 0, there must be a periodic boundary in the topology file.
Constant
pressure is not used in minimization (IMIN=1, above).
For a periodic system, constant pressure is the only way to equilibrate
density if the
starting state is not correct. For example, the solvent packing scheme used
in LEaP
can result in a net void when solvent molecules are subtracted which can
aggregate
into "vacuum bubbles" in a constant volume run. Another potential problem
are
small gaps at the edges of the box. The upshot is that almost every system
needs
to be equilibrated at constant pressure (ntb=2, ntp>0) to get to a proper
density.
But be sure to equilibrate first (at constant volume) to something close to
the final
temperature, before turning on constant pressure."
I notice that the tutorial states that temperature & density are being
equilibrated together. Was this discovered through trial & error? Therefore,
will it have to be re-evaluated for every different system? Are there
general rules when you know that you will invariably have to do two separate
equilibration steps for density & temperature?
Thank you for an assistance you may be able to provide.
best regards,
GT
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Received on Wed Jul 07 2010 - 11:30:03 PDT
