Dear professor Roe,
Thank you very much for your advice , I would check the both possibilities
to find the source of the error.
Greeting,
Hector
> Hi,
>
> Based on the picture I can think of two possibilities:
>
> 1) The system coordinates have been rotated (via e.g. an RMS best-fit)
> prior to imaging. The rotation essentially invalidates the unit cell
> vectors for those coordinates and the imaging is thus invalid. The
> solution
> is to make sure any rotations occur after imaging. I think this the most
> likely.
>
> 2) The system density is off for some reason and needs to equilibrate
> further via simulation in NPT ensemble.
>
> -Dan
>
> On Wed, May 13, 2020 at 3:46 PM Hector A. Baldoni <hbaldoni.unsl.edu.ar>
> wrote:
>
>> Dear amber users,
>>
>> In the attached link appears the image of the water box after running
>> autoimage in cpptraj ambertools20. Why are some waters not imagined back
>> to the original box and how can this problem be solved?
>>
>>
>> https://drive.google.com/file/d/1LrQ6QmRvp2xWiLef-f3hJMgzmLI5bPpO/view?usp=sharing
>>
>> Any insight would be most greatly appreciated.
>> Cheers,
>> Hector
>>
>>
>> --------------------------------------
>> Dr. Hector A. Baldoni
>> Profesor Titular (FQByF-UNSL)
>> Investigador Adjunto (IMASL-CONICET)
>> Area de Quimica General e Inorganica
>> Universidad Nacional de San Luis
>> Chacabuco 917 (D5700BWS)
>> San Luis - Argentina
>> hbaldoni at unsl dot edu dot ar
>> Tel.:+54-(0)266-4520300 ext. 6157
>> --------------------------------------
>>
>>
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>>
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>
--------------------------------------
Dr. Hector A. Baldoni
Profesor Titular (FQByF-UNSL)
Investigador Adjunto (IMASL-CONICET)
Area de Quimica General e Inorganica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------
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Received on Wed May 13 2020 - 17:00:02 PDT
