I believe setBox makes no attempt to reorient the molecule, so if
it's rotated slightly, the box would be bigger.
Bill
Chinthaka Ratnaweera <cnr88.msstate.edu> wrote:
> Thanks for the idea. I didn't know about the setbox command before. But
> after running setBox command (without any other commands) I got somewhat
> larger box dimensions.
>
> My original box size in inpcrd file is 168.0124930 143.1571890 154.5810580
>
> Now it is 197.0260000 164.0260000 177.0260000
>
> I used " setBox <unit> vdw " command in leap input
>
> I don't see any expansion in the box side by visualizing in VMD. Will this
> matters in simulation.
>
> Thanks
>
> Chinthaka
>
> On Mon, Dec 17, 2012 at 7:53 AM, Jason Swails <jason.swails.gmail.com>wrote:
>
> >
> >
> > On Dec 17, 2012, at 1:07 AM, Chinthaka Ratnaweera <cnr88.msstate.edu>
> > wrote:
> >
> > > Thanks, But I think I need the periodic boundary conditions for the
> > > simulation. Just adding ethanols will not create periodic box
> >
> > Look at the setBox command in tleap-- that will add a box around the
> > system without adding any atoms.
> >
> > HTH,
> > Jason
> > >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Chinthaka Nadun Ratnaweera
> Hand Lab Rm 1126
> Mississippi State University
> 310 Presidents Circle
> Starkville, MS 39762
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Received on Mon Dec 17 2012 - 17:00:02 PST
