Yes '5' is the closeness .But I assumed it will be rectified while I run my
constant pressure dynamics.
I will construct a new box and work it out.
How to align it square to the axes, is that in xleap .
In packmol I used center of mass to keep my polymer at center of the box.
Thanks
John
On Fri, Jan 28, 2011 at 2:02 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > > > set box x vdw 5
>
> I forget what the '5' would mean, but maybe it's contributing to
> the large initial box. Another way a box might be too large is
> if the initial model isn't aligned square to the axes.
>
> Bill
>
> _______________________________________________
> 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 Fri Jan 28 2011 - 13:00:02 PST
