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reuter-group / webnma3

Fast normal mode calculation and analyses for protein structures
http://apps.cbu.uib.no/webnma3/
GNU General Public License v3.0
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Calculation of frequencies associated with each mode #2

Closed purvi24 closed 2 years ago

purvi24 commented 2 years ago

Dear,

I am trying to calculate the frequency associated with each mode using the eigen values using the formula: Frequency. = sqrt(EigenValue) However, the values obtained doesn't correlate well with the literature. I suspect there is an issue with the unit conversions. Could somebody assist me with exactly how to obtain the absolute frequency values?

Greetings, Purvi Gupta

Ginko-X commented 2 years ago

Hi Purvi, Sorry for the late reply. As I mentioned in the email, the frequency can be calculated as

where e is the eigenvaule in the modes.txt file, and f the vibrational frequencies.

In addition, the transformation between the raw modes v (in the modes.txt file) and the vibrational modes V is:

where M is the protein's mass, k is constant (=1.3806513e-23 * 6.0221367e23 / 1000), and T is the temperature (=300).

I didn't find this calculation detail from WEBnma's publications, but you may find more from Konrad Hinsen's work and the source code of MMTK (earlier versions of WEBnma used MMTK to calculate the normal modes):

Hinsen, Konrad. "Normal mode theory and harmonic potential approximations." Normal Mode Analysis. Chapman and Hall/CRC, 2005. 25-40.

Hinsen, Konrad. "Analysis of domain motions by approximate normal mode calculations." Proteins: Structure, Function, and Bioinformatics 33.3 (1998): 417-429.

I hope this helps, and feel free to ask if you have further questions.

Ginko-X commented 2 years ago

As no further question posted I just close this issue.