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Hello Nikolai--
> coor rgyr sele=( all ) end
> coor translate vector=(-$XCM,-$YCM,-$ZCM) end
> end loop write
> ----------------------------------------------------------------------
>
This will only translate the final frame of your trajectory- and after
it is written to file.
> It also seems that post-processing would not help in this case,
> since the protein quickly flies out of the 999A box, and the
> trajectory becomes garbled (dcds are written in a strange order and
> cannot be converted to .pdb).
>
It sounds like there is a large initial center of mass velocity. You can
subtract this out with the following snippet of python code placed
before the dynamics statement:
cpyth "from vec3 import Vec3"
cpyth "vel=Vec3(0,0,0)"
cpyth "for atom in AtomSel('all'): vel += atom.mass() * atom.vel()"
cpyth "M=0"
cpyth "for atom in AtomSel('all'): M += atom.mass()"
cpyth "vel /= M"
cpyth "for atom in AtomSel('all'): atom.setVel( atom.vel() - vel )"
best regards--
Charles
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