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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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFGZGJsPK2zrJwS/lYRAkpQAJ0Zbst6hlhI3QZiWt9pnlWnI139ZACfXgjL PMbChnVnaZTbp5QoLUdo+/Y= =zZ4t -----END PGP SIGNATURE-----
