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 Thu Sep 04 2014 - 05:30:03 PDT
