Did you set the box conditions in tkconsole of VMD? Tail the last .rst
file to get the box info and put that in tkconsole as follows:
pbc set {X Y Z a b c}
where X,Y,Z are the box lengths in each direction that should be X=Y=Z in
truncated octahedron box with a=b=c=109.4712190.
After this, turn on the preiodicity in Graphical Representations.
Ilyas Yildirim, Ph.D.
-----------------------------------------------------------
= Department of Chemistry - 2145 Sheridan Road =
= Northwestern University - Evanston, IL 60208 =
= Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
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-----------------------------------------------------------
On Tue, 26 Feb 2013, Jason Swails wrote:
> On Tue, Feb 26, 2013 at 9:10 PM, 吴云剑 <yunjian.wu.hotmail.com> wrote:
>
>>
>> Does any one know how VMD display periodic image of an octahedron box? In
>> my simulation, my enzyme is on one side of octahedron box and ligand
>> molecule on the other side. I assume one is binding with another in
>> neighbouring box.
>> I've tried "Graphical Representations" -> "Periodic", but it does not show
>> correctly.
>>
>
> If that doesn't work, I'm not sure what will (if anything). This question
> is probably better asked on the VMD mailing list.
>
> One option is to reimage your trajectory using cpptraj. With a fully
> up-to-date AmberTools 12, use the "autoimage" command to center your
> protein and ligand in the water box.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Feb 26 2013 - 19:30:02 PST
