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Hello Nah--
> How can I save the trajectory of the Molecular Dynamics simulation ?
> for ex., how can i take snapshots at various temperatures (2000,1000,500,100
> etc.,) if not the whole trajectory,when running the refine.py (example script
> from eginput/protG dir) ?
>
The IVM does not currently have a facility to write out a trajectory
file- it is on the todo list. However, it is possible to visualize
trajectories by directly writing frames to VMD-XPLOR. To do this, place
the following after the dyn object is created:
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 )
Then, a trajectory will appear in a running instance of VMD-XPLOR. You
may need to specify the -port (and -host if you're running VMD-XPLOR and
Xplor-NIH on different computers) option to the xplor command. To figure
out the correct value for -port, start VMD-XPLOR, and select:
Control --> Info
hope this helps--
Charles
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