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 - 06:00:08 PDT
