VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Fri Nov 30 2007 - 09:50:33 CST

Dear VMD experts,

I have a very long simulation of an 8-residue peptide, and would like to see
the (phi,psi) angle of each residue as a function of time. I am trying to
use VMD's 'Timeline', and I face these issues:

a) On first loading my .psf, then opening Timeline, I choose File>print to
file; Calculate>phi; Appearance>(color purple and the angle range). Then I
load my .dcd file. However, nothing happens in the time line viewer, and the
file written out is also a blank file. Can I get some pointers here, as I
did not find instructions in the VMD User's guide?

b) Are purple and yellow the only colors available?

c) I find it a little unusual that it can calculate (delta_Psi), but not
just the dihedral psi... are they the same? If not, is there a way I can get
the timeline for the Psi angle too?

Thanks in advance,
Regards,
Neelanjana Sengupta 

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