Hi Charles, Ramon:
Many thanks!
This solution did not work for me, though (it's conceptually similar to
what we tested before - although nicer). Below is the code, as suggested
by Ramon:
-------------------------------------------------------------------------------
evaluate($count=1)
while (2>1) loop write
evaluate ($TRAJECTORY = "traj_"+encode($count)+".dcd")
dynamics torsion
ntrfrq = 0
timestep = 0.002
nstep = 5000
tcoupling = true
tbath = 300
nprint = 500
iprfrq = 0
asci = false
nsavc = 500
traj = $TRAJECTORY
end
evaluate ($count=$count+1)
coor rgyr sele=( all ) end
coor translate vector=(-$XCM,-$YCM,-$ZCM) end
end loop write
----------------------------------------------------------------------
The log looks fine, i.e. it shows that the center of mass has been
determined and the translation executed. But when you look at the
coordinates (via vmd or by eye), it's as if nothing has happened -- the
protein just flies away, and no translation takes place...
It's as if "dynamics torsion" procedure stores the last frame before
the dump, and then restarts from this same frame (ignoring our attempts
to reset the main coordinate set in the interim). Is this an unexpected
behavior, or am I just unaware of some fundamental xplor conventions...?
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).
Once again, many thanks and cheers!
Nikolai
Charles at Schwieters.org wrote:
>Hello folks--
>
>
>
>>Centre of mass option:
>>-----------------------
>>{*calculate centre of mass vector *}
>>COORmanipulation RGYRation SELEction=(all) end
>>!vector stored under $XCM,$YCM,$ZCM
>>
>>{*Translate to origin*}
>>COORmanipulation TRANslate VECTor (-$XCM,-$YCM,-$ZCM)
>>
>>
>>
>
>This or an analogous solution is the only way to remove translational
>motion without subtracting out rotation. There should be postprocessing
>tools which subtracts out the center of mass position from each frame of
>a trajectory. On the other hand, fixing an atom is not suggested- it
>will cause various artifacts and distort motion in many degrees of of
>freedom, including rotation.
>
>best regards--
>Charles
>
>
--
Nikolai R. Skrynnikov
Assistant Professor
Department of Chemistry
Purdue University
560 Oval Drive
West Lafayette, IN 47907-2084
USA
phone: 765 - 494 8519
fax: 765 - 494 0239
e-mail: nikolai at purdue.edu
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