usage: setBox <unit> vdw|centers [ clearance | <clearance_xyz_list> ]
As I remember it, setBox takes the unit and, without reorienting
it, uses either vdw boundaries or atom centers to draw a box with
an optional clearance in all directions or an optional list of
clearances in the x,y,z directions. If the box is already equilibrated,
the vdw option would introduce voids at the edges which would take
more equilibration than otherwise, but since the system needs to be
warmed up anyway, this is probably not a factor.
Bill
Albert <mailmd2011.gmail.com> wrote:
> Hello Jason:
> thank you very much for your kind helps.
> I generate the system from CHARMM GUI and it contains solvent, ions
> and protein for a full MD system, then I import it into tleap to
> generate Amber input file. I've obtained the periodic information such as:
>
> CRYST1 59.566 59.566 96.412 90.00 90.00 90.00 P 1 1
>
> I don't find detailed comments for this 'setBox' in the manual or online
> tutorial expect helps from tleap:
>
> usage: setBox <unit> vdw|centers [ clearance | <clearance_xyz_list> ]
>
> do you have any idea how should I use this command correctly? Probably
> like the following?
>
> setBox 0 0 0 59.566 59.566 96.412
>
>
>
>
> On 05/09/2012 09:41 PM, Jason Swails wrote:
> > You can use the "setBox" command in tleap to add periodic box information.
> > If you add a solvent box, this should be done automatically.
> >
> > HTH,
> > Jason
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 09 2012 - 14:00:04 PDT
