On Sun, Jan 27, 2013 at 6:57 AM, Thomas Evangelidis <tevang3.gmail.com>wrote:
> Dear AMBER community,
>
> I have run a long simulation leaving iwrap and ntxo to their default values
> (iwrap=0, ntxo=1). However, I just read in the manual that for very long
> runs, setting iwrap = 1 may be required to keep the coordinate output from
> overflowing the trajectory and restart file formats, especially if
> trajectories are written in ASCII format instead of NetCDF. This is exactly
> what happened in my case, waters and ions have diffused way too long and
> I'm afraid that apart from performance slow down I may encounter serious
> problems in the future as I prolong my simulation.
>
> Will there be any compatibility issues that are not obvious to me if I
> switch to iwrap=1 and ntxo=2 from this point?
>
There should be no compatibility issues. I would also strongly suggest
switching to ioutfm=1 (NetCDF trajectories), since there is almost no good
reason not to. The ASCII trajectory will overflow as soon as the ASCII
restart will...
Note, if you switch to ntxo=2 (and ioutfm=1), you don't necessarily need
iwrap=1.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Jan 27 2013 - 06:30:03 PST
