this is no problem. use iwrap=1 and the ptraj center and image commands to
fix things before rmsd. it works fine. the only reason to turn off wrapping
is if you want to study diffusion.
2010/4/7 Jacky Zhao <jackyzhao010.gmail.com>
> I'm looking forward the answer for this question, too:)
>
>
>
> 在 2010-4-8，7:03，Emmanuel Baribefe Naziga <baribefe.gmail.com> 写到：
>
> Hi Everyone,
>>
>> I intend to start some long simulations and I am concerned about
>> overflow when amber writes trajectories (getting *** symbols)
>>
>> I understand that I can use iwrap=1 to wrap coordinates back into the
>> original box but I know that in the simulation time my solute will move
>> out
>> of the box several times and I want to avoid issues with RSMD etc
>> afterwards.
>>
>> Is there a way to overcome this short of stopping every now and then and
>> restarting? I would prefer to have one trajectory instead of several
>> restarts.
>>
>> Any ideas or comments very welcome.
>>
>> Thanks
>>
>> Emmanuel.
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Wed Apr 07 2010 - 18:30:03 PDT
