Re: [AMBER] iwrap on very long simulation

From: David A Case <>
Date: Thu, 4 Sep 2014 08:01:17 -0400

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.


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Received on Thu Sep 04 2014 - 05:30:03 PDT
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