Hello everybody,
I'm having what seems to be a system imaging problem, and I'm not able to
solve it.
I'm performing a pretty long trajectory (70 ns) on a protein dimer with two
non-protein substrates (4 solute molecules). I performed it with PME in a
cubic box and with iwrap=1.
The question, is that when performing the rmsd analysis, it leads to
unrealistic results. As recommended in the list, I tried to center the
image. The ptraj script that I employed is:
reference tic.rst7
trajin tic_md_1.mdcrd 1 10000 200
center :1-217 mass origin
image origin center
center :1-434 mass origin
image origin center
center :1-435 mass
image origin center
center :1-436 mass
image origin center
rms reference out tic_md_rmsd_new.dat .CA,C,N
And the output is attached.
Any suggestion?
Thanks in advance
Alex
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Received on Tue May 10 2011 - 09:30:03 PDT
