> 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.
...
> 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
It could be that you do not always center to the origin... Otherwise, if
the periodic box is not particularly large (i.e. there is not a lot of
water around the protein) the imaging can be pathological (meaning that
the substrate is already closer to the periodic image than the main image.
I would think that the first two imaging commands alone should work, i.e.
image dimer1, then image dimer1+dimer2. If the substrates are indeed
imaged into a different unit cell, the two imaging commands "should"
work (assuming dimer 1 is residues 1-217, and including dimer2 leads to
residue 434), i.e.:
center :1-217 mass origin
image origin center
center :1-434 mass origin
image origin center
Alternative tricks are to avoid the "center" in the image command (which
images based on the first atom I think). Given the frequency of this
issue on the reflector, perhaps I should add a smart imaging routine that
allows users to specify what molecules should be together; this would be
useful for small or very tightly packed unit cells.
--tec3
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Received on Tue May 10 2011 - 09:30:04 PDT
