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Hello Gary--
>
> Using the PS statement can I can monitor in vmd the state
> of an xplor dynamics calcualtion as it is going on in real time? or do I
> have to monitor trajectories after the fact.... [Of course what I want
> to do is monitor a dynamics run as it is going to see if my new protocol
> is doing resonable things wihhout creating a trajectory file...] and
> having to wait till the end of the run
>
you can monitor dynamics during the simulation.
Within the old XPLOR interface you can achieve course-grain
visualization using the method of eginput/protG/anneal.inp: this
updates the VMD structure after each DYNAmics INTErnal
statement. [Finer grain visualuzation could be achieved by reading
from a trajectory file written during each dynamics interval.]
Better support is available in the Python interface:
from vmdInter import VMDInter
from vmdInter import VMDTraj
vmd=VMDInter()
vmdStruct=vmd.makeObj("dynStruct"); vmdStruct.bonds( AtomSel("not hydro") )
vmdTraj=VMDTraj(vmdStruct); vmdTraj.saveInterval=5
dyn.setTrajectory( vmdTraj )
where dyn is an IVM.
please let me know if you'd like more details.
regards--
Charles
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