On Thu, Jun 21, 2012 at 1:33 PM, Brandon Sim <simpavid.gmail.com> wrote:
> Dear Jason,
>
> I didn't change the topology file at all, only the input coordinate file
> (and only to add the size of the box at the bottom). Will this cause
> problems? The minimization in sander seemed to proceed without problems,
> but I'm not sure. The solvent box is a cube, and I am minimizing under no
> pressure regulation (ntp = 0)
>
I don't know if it will cause problems or not -- I never run periodic
simulations without PBC info in the topology file. I would imagine that if
any problems did occur, they would be fairly obvious, but I'm not sure.
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jun 21 2012 - 11:00:03 PDT
