Hi,
On Mon, Apr 13, 2015 at 10:42 PM, pooja chahal
<chahal.pooja.rs.gmail.com> wrote:
> Also one more thing that I am observing is that while generating .pdb files
> using ptraj with unwrap command, some of atoms attains a very high negative
> value (< -1000) for coordinates. For these coordinates "********" appears
> in the .pdb file instead of real coordinates. However, this is not the only
This seems odd to me. The multiple asterisks is something that fortran
code does for numerical overflow, not C/C++ code (to my knowledge).
You shouldn't be getting asterisks in your PDB files if you're
creating them with ptraj. Do you get the same behavior with cpptraj?
If on the other hand you mean you see asterisks in the original ASCII
trajectory file then your coordinates overflowed during your
simulation and there is no way to recover them. For this reason it is
recommended that during simulations you use 'iwrap=1' to enable
imaging, 'ioutfm=1' to write NetCDF trajectories, and 'ntxo=2' to
write NetCDF restart files; the NetCDF file format is not nearly as
susceptible to issues as the ASCII format.
Hope this helps,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Apr 14 2015 - 07:30:03 PDT
