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 - 08:00:04 PST
