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 20:25:28 +0800 (CST)

I have rerun the dynamic simulation, with less often output. Now, a half of the large trajectory is obtained. The results seem reasonable, and not change so much. It seems that data accurecy is so important in MD simulation.

>and gradual release of restraints

I have read Tutorial A4:NMR Refinement of a DNA Duplex. Is this enough to performing a simulation with gradual release of restraints. Would you please introduce me some references about gradual release of restraints.

Thank you all for the help, best regards!

Jianing



2010-04-14 10:46:52"Carlos Simmerling" <carlos.simmerling.gmail.com> д
>i agree that you should be using a series of simulations with slow heating
>and gradual release of restraints. if not, it's not at all surprising that
>some simulations completely unfold.
>
>
>2010/4/13 Jianing <song_jianing_hi.126.com>
>
>> 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 Wed Apr 14 2010 - 05:30:02 PDT
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