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

From: Jianing <song_jianing_hi.126.com>
Date: Wed, 14 Apr 2010 10:44:33 +0800 (CST)

Hi Bill,
After the system has been heated to 300K with the solute fixed in 100ps, the keyword 'irest=1' instead of 'irest=0' should be reasonable when perform the next equlibration for 5ns. I have checked the structure after equlibration, it sounds reasonable, similar to the XRD structure of villin headpiece. But I will change the value of irest to 1 to see the difference and maybe this is the reason for my strange results, you know,
 small error accumulates into big mistake.
>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? But equlibration is to make the system equilibrated and don't corelate to the initial structure. If you put constraints on the system, is this too manual and don't leave the system where it is.
Thank you in advance.
Jianing
 
 
 




2010-04-14 00:57:28"Bill Ross" <ross.cgl.ucsf.edu> д
>This mdin seems like a fast-warming regime that I would hesitate to
>even call equilibration:
>
> irest = 0,
> ...
> tempi = 300.0,
> temp0 = 300.0,
>
>Have you looked at your structure to see if it's reasonable?
>Normally one equilibrates by slow warming and/or keeping the
>solute fixed with restraints.
>
>It will be interesting to see how replicable your results are
>in the parallel execution situation.
>
>Bill
>
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Received on Tue Apr 13 2010 - 20:00:03 PDT
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