AW: spectrum simulation

From: Norman Geist (
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.


Good luck

Norman Geist.


Von: [] Im Auftrag von francesco oteri
Gesendet: Sonntag, 24. Februar 2013 21:57
An: namd-l
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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