[Xplor-nih] lshi at chem.umn.edu

[Charles at Schwieters.org]

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Hello Lei--

>    I am wondering if there is a way to generate a trajectory from the
> simulation using xplor-nih.I need it for visualization purpose.
>    I was reading the following message in the mailinglist,
>    http://nmr.cit.nih.gov/pipermail/xplor-nih/2004-June/000196.html
>    Is it done in the same way? Can I find an example script somewhere?

yes. That mechanism will send a trajectory to VMD-XPLOR. You just place
the following at the beginning of your script:

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

and for each IVM object (called ivm here) place

ivm.setTrajectory( vmdTraj )

after it is created.

VMD-XPLOR should be running for this to work.

Alternatively, if you're using the XPLOR interface, you can create a DCD
file using the TRAJ statement within the DYNAmics INTErnal statement.

best regards--
Charles
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