Thanks a lot. I have adding "iwrap=1" in the begin of the heating process. Would you mind to give me some suggestions when I open the iwrap ?
Thanks a lot.
Jacky
> Date: Mon, 28 Dec 2009 10:44:38 -0500
> Subject: Re: [AMBER] .rst file error
> From: jason.swails.gmail.com
> To: amber.ambermd.org
>
> Hello,
>
> I believe adding iwrap=1 will fix your problem. This will wrap any
> particle leaving the original box back into that box, which should
> prevent diffusional processes from moving a particle beyond to a
> position too large to be included in the restart file (thus resulting
> in *******s).
>
> Good luck!
> Jason
>
> 2009/12/28 ZhaoLei <jackyzhao010.hotmail.com>:
> >
> > Ms. Xu
> > Thank you for your immediately reply. Would you think that adding "iwrap=1 " in our simulation could solve my problem? According to your suggestion, I have resimulated the complex. We have simultaneously simulated the protein in another PC workstation, when I performed this simulation. But the error occur at 40ns, would you think that just repeat the simulation process with the same input file could solve this problem?
> > In addtion, would anyone give me some detail information about the reason that the error occur in the rst file.
> >
> > Thank you for taking your time and best regards:)
> >
> > Jacky
> >
> >> Date: Mon, 28 Dec 2009 16:00:57 +0800
> >> Subject: Re: [AMBER] .rst file error
> >> From: xujia.ruc.gmail.com
> >> To: amber.ambermd.org
> >>
> >> Dear Jacky,
> >>
> >> There is "*********" in your rst file. This error sometimes
> >> happens in long-term simulation, and to the best of my knowlegde
> >> currently it can not be solved. You should go back to a former correct
> >> rst file, such as 30ns or earlier, and re-simulate. Possibly it will
> >> be fine.
> >>
> >> Best regards,
> >> Jia Xu
> >>
> >> 2009/12/27 ZhaoLei <jackyzhao010.hotmail.com>:
> >> >
> >> >
> >> >
> >> >
> >> > Dear everyone
> >> >
> >> >
> >> >
> >> > I am performing a long-term protein dynamic simulation. But
> >> > in the process, I have come across an error. I have read the log file,
> >> > which indicates the .rst file may occur an error. I have performed this
> >> > simulation again. But the problem is still in there. Could you mind to
> >> > give me some suggestions to solve this problem?
> >> >
> >> >
> >> >
> >> > Thanks very much:)
> >> >
> >> > Jacky
> >> > _________________________________________________________________
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>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
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Received on Mon Dec 28 2009 - 18:00:04 PST
