On Sat, Dec 06, 2014, Sylvester Tumusiime wrote:
>
> When using the addtobox command, there is the -X -Y -Z flag requirements.
>
> I would like to find out how one can determine good starting arbitrary
> numbers to use when using addtobox.
>
> I have tried some values and my solute is out of the water cube.
In AddToBox, you must already know the size of the box, which you input on the
command line. It was originally written to support crystal simulations, where
the unit cell size is known. These cannot be "arbitrary numbers".
Having the solute "out of the water cube" sounds like an imaging problem: try
using the autoimage command in cpptraj to pack everything into a contiguous
unit cell.
...good luck....dac
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Received on Sat Dec 06 2014 - 06:30:02 PST
