After about a 720 picosecond simulation of a prmtop and inpcrd file created
by AMBER from a pdb created in spartan '08 in OpenMM I get a pdb file
showing the simulation that is visualized with VMD.
At 360 picoseconds teh molecule seems to go out of the box of water and I
was told it was an imaging issue and to use autoimage in cpptraj to
restructure to output the simulation correctly.
When I try to run autoimage I get "Warning: Unknown Command autoimage."
Here is the commands to get the prmtop and inpcrd files:
http://pastebin.com/raw.php?i=63sFFQ6q
and here are the commands i tried to run autoimage (outputPyMol.pdb is the
file created by OpenMM): http://pastebin.com/raw.php?i=6R9VNvFp
Thank you for your time, it is very much appreciated!
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Received on Fri Feb 08 2013 - 21:00:02 PST
