From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Feb 25 2013 - 01:01:05 CST
well as far as I know, you can compute a infrared spectrum out of a fine grained and long trajectory, don’t you? If you don’t want to do it on your own, use the VMD plugin. It’s located within the menu Extensions->Analysis->IR Spectral Density Calculator.
No idea about the other stuff.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von francesco oteri
Gesendet: Sonntag, 24. Februar 2013 21:57
Betreff: namd-l: spectrum simulation
Dear namd users,
I have been studying the association between a protein and an electrode by MD simulation. In particular I am interested in the relative orientation in respect to the surface.
I only have the PM-IRRAS spectrum of the complex.
I am wondering if someone knows a method or a software that simulate the PM-IRRAS spectrum or the infrared spectrum of a protein.
Thank you in advance,
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