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.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.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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>>>>>
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>>
>>
>> --
>> ---------------------------------------
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-4032
>>
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>
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Received on Mon Dec 28 2009 - 18:30:06 PST
