Dear Amber users,
I have a question about processing a trajectory, run using periodic boundary conditions, with ptraj.
I wish to center and image a trajectory with the following command:
trajin file_in.mdcrd 1 2500 1
center origin
image familiar origin
trajout file_out.traj
When I use Amber 10 to perform this the resulting output trajectory loses the original box size information, instead each frame has the box size as given in the prmtop. However if I use Amber 7 the output trajectory keeps the original box size (which changes slightly with each frame as I am doing an NPT run). Is there an option with Amber 10 to keep the original box size with each frame?
Kind regards,
Callum Dickson
Phd Student
Institute of Chemical Biology
Imperial College London
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Received on Wed Oct 13 2010 - 03:30:03 PDT
