> 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 - 16:30:05 PDT
