The right way to simulate in principle is to pack the actual unit cell,
so there'd only be one copy of your structure, which would rely on Ewald
for terms from summed images. If you wanted more copies you'd have to
replicate the unit cell, which might require other software. But even
then you'd have to make sure the aggregate cell was supported by Amber,
which is geared more toward solvation than crystal simulations. If you
solvate the molecule with itself using leap, you will get a lattice of
molecules bearing no relation to the crystal structure.
Bill
On 4/12/2015 11:30 AM, jacob wick wrote:
> Dear all,
>
> I have a crystal structure of an organic molecule from crystallographic
> database. I want to see how the molecule will look like in packed state
> (arrangement of the molecules in 3-D) i.e. when it is not alone but in the
> presence of many such molecules in the solid packed state.
>
> I am not getting any references for performing such study but one way which
> I can think about is:
>
> 1. Creating .frcmod, .prepin and .lib file of that molecule.
> 2. In tleap, Using solvateoct command, constructing a box having many
> copies of that molecule and equilibrating the box.
>
> Is it the right way to perform the desired study? Please suggest.
>
> Thanks,
> Jac
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Received on Sun Apr 12 2015 - 17:30:02 PDT
