Dear Prog. Case
thank you for your answer.
On Thu, Sep 4, 2014 at 7:01 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Thu, Sep 04, 2014, Setyanto Md wrote:
> >
> > I read at the amber 12 manual book on page 20, in the section of iwrap.
> > It is mention "..For very long runs, setting iwrap = 1 may be required to
> > keep the coordinate output from overflowing the trajectory and restart
> file
> > formats,..."
> >
> > How long of the simulation can be count as very long simulation ?
>
> There is no general answer to this question: it depends a lot on the
> nature of
> the solute and the size of the simulation box.
>
> > For iwrap=0, can we make it wrap again after simulation, maybe with some
> > process ?
>
> The cpptraj program can "unwrap" trajectories that have been wrapped.
> Another
> useful strategy is to set ntxo=2 (using the netcdf restart format), which
> does
> not have the problem of overflowing a fixed field length.
>
> ....dac
>
>
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Received on Sat Sep 06 2014 - 18:00:03 PDT
