Googling "amber *s in restart" provides this as the first hit:
http://archive.ambermd.org/201009/0473.html
This is caused in long simulations when atoms diffuse too far away for the
number to fit in the fixed-format field in the restart file. There are 2
solutions:
1) use the ntxo=2 flag (in Amber 12) to trigger NetCDF restart files which
do not have this limitation.
2) use iwrap=1 in order to wrap coordinates into the same periodic box.
I typically use both options, since NetCDF restarts are safer and faster to
write and contain full double-precision values, and iwrap=1 keeps the
coordinate values at a minimum value (thereby improving numerical precision
for cpptraj analysis and keeping all atoms in the same periodic cell). The
'unwrap' command in cpptraj can undo the effect of wrapping.
HTH,
Jason
On Thu, Jun 13, 2013 at 8:10 PM, Edward Pate <edpate.hotmail.com> wrote:
> I tried to restart an amber 11 simulation. I got the error message that
> the .restart file could not be read. The restart file contains only
> position information. I looked more closely at the .restart file and some
> of the position coordinates have the value ********. I would greatly
> appreciate it if someone could point me in the right direction to resolve
> the problem.
>
> Thanks,
>
> Ed
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jun 13 2013 - 18:30:02 PDT
