AMBER Archive (2009)

Subject: RE: [AMBER] .rst file error

From: ZhaoLei (jackyzhao010_at_hotmail.com)
Date: Mon Dec 28 2009 - 04:36:17 CST

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_at_gmail.com
> To: amber_at_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_at_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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