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

From: Jianing <song_jianing_hi.126.com>
Date: Thu, 15 Apr 2010 09:33:07 +0800 (CST)

ok, got you. Thanks, Bill, best wishes!
Jianing




2010-04-15 00:38:23"Bill Ross" <ross.cgl.ucsf.edu> д
>> >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.
>
>Bill
>
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Received on Wed Apr 14 2010 - 19:00:02 PDT
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