(unknown charset) Re: [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration

From: (unknown charset) 冉挺 <rantingjing0445019.gmail.com>
Date: Sat, 10 Jul 2010 10:52:33 +0800

As the manual script shows, constant V equ is essential to place the adding
solvate to reasonable positions and regulate the temperature at the same
time. I have make a trail to directly heat the system after minimization
with constant pressure, but this work failed for some atoms with unlimited
rate (*****). I assume the heat precedure makes the system unstable when it
go along with constant pressure.
On Thu, Jul 8, 2010 at 2:07 AM, g t <sketchfoot.gmail.com> wrote:

> 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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> AMBER.ambermd.org
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Phar.M.Ran Ting
Molecular-Design &  Drug-Discovery Lab
Laboratory Building A212
639 Longmian Avenue
Nanjing, 210009
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Received on Fri Jul 09 2010 - 20:00:03 PDT
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