Thanks Bill.
Emmanuel
On Wed, Apr 7, 2010 at 5:11 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > I understand that I can use iwrap=1 to wrap coordinates back into the
> > original box but I know that in the simulation time my solute will move
> out
> > of the box several times and I want to avoid issues with RSMD etc
> > afterwards.
> >
> > Is there a way to overcome this short of stopping every now and then and
> > restarting? I would prefer to have one trajectory instead of several
> > restarts.
>
> I don't think stopping and restarting will help anything (except breaking
> up a run can save problems from restarting from scratch after a crash).
>
> I believe you are pretty much forced to use iwrap=1 and ptraj to image
> everything, tho you can keep the solute from moving 'far' by removing
> net momentum periodically.
>
> Bill
>
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Received on Wed Apr 07 2010 - 17:00:03 PDT
