AMBER Archive (2009)

Subject: RE: [AMBER] .rst file error

From: ZhaoLei (jackyzhao010_at_hotmail.com)
Date: Mon Dec 28 2009 - 20:57:34 CST

Thank you very much :)

Jacky

> From: jason.swails_at_gmail.com
> To: amber_at_ambermd.org
> Subject: Re: [AMBER] .rst file error
> Date: Mon, 28 Dec 2009 21:09:04 -0500
>
> Hello,
>
> It is natural to see the protein moving out of the center of the box
> during the simulation, and this does not present a problem. It is
> simply a visualization limitation as only a single box is displayed.
> However, the rest of the molecules in every other box is included in
> the actual calculation. You can use ptraj image command to put the
> protein back in the center of the box for visualization.
>
> Good luck!
> Jason
>
> On Dec 28, 2009, at 8:37 PM, ZhaoLei <jackyzhao010_at_hotmail.com> wrote:
>
> >
> > 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_at_gmail.com
> >> To: amber_at_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_at_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_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
> >>>>> _________________________________________________________________
> >>>>> 立刻下载最新版 Windows Live Messenger！
> >>>>> http://www.windowslive.cn
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER_at_ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER_at_ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>> _________________________________________________________________
> >>> MSN十周年庆典，查看MSN注册时间，赢取神秘大奖
> >>> http://10.msn.com.cn
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER_at_ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >>
> >> --
> >> ---------------------------------------
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Graduate Student
> >> 352-392-4032
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER_at_ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _________________________________________________________________
> > 立刻下载最新版 Windows Live Messenger！
> > http://www.windowslive.cn
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
                                               
_________________________________________________________________
立刻下载最新版 Windows Live Messenger！
http://www.windowslive.cn
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber