Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?

From: Bill Ross <>
Date: Wed, 14 Apr 2010 09:38:23 -0700 (PDT)

> >Normally one equilibrates by slow warming and/or keeping the
> >solute fixed with restraints.
> what's the exact meaning of this? Do you mean that equlibration should
> performed with restraints generally?

Initial warming is often performed with restraints on the solute,
to allow the artificial water structure to arrange itself around
the often-empirical solute structure. Then in the later stages
the restraints are removed and the whole system is allowed to
equilibrate together.

> But equlibration is to make the system equilibrated
> and don't corelate to the initial structure.

There's nothing wrong with correlation to the initial structure, in
my opinion. What one is looking for is reasonable velocities.

> If you put constraints on the system, is this too manual and don't
> leave the system where it is.

It compensates for the artificiality of the solvation method.


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Received on Wed Apr 14 2010 - 10:00:03 PDT
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