I will follow your advice to find out some articles about gradual release of restraints.
Thank you very much!
Jianing
在2010-04-14 20:37:48，"Carlos Simmerling" <carlos.simmerling.gmail.com> 写道：
>as always, the best approach is to find articles in the peer-reviewed
>literature that are sucessful at the type of study that you wish to do, and
>follow their protocols.
>
>2010/4/14 Jianing <song_jianing_hi.126.com>
>
>>
>>
>>
>> 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
>>
>>
>>
>> 在2010-04-14 10:46:52，"Carlos Simmerling" <carlos.simmerling.gmail.com> 写道：
>> >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
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> 在2010-04-14 00:57:28，"Bill Ross" <ross.cgl.ucsf.edu> 写道：
>> >> >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 - 06:30:03 PDT
