NMA difference between NMA and AANMA algorithm

[Mamta Mohan]

Hello,

I am taking Normal Mode analysis tutorial.

I would like to know the difference between two approaches.

I am also interested in NMA via Gaussian Network Model and Anisotropic Network Model.

I do see GNM in recent update but I do not see ANM. Shall I understand ff ANM is analogues to ANM model.

NMA tutorial talks about deformation and fluctuation calculation for nma. Are they available for GNM and ANM (model available).

In the documentation these fuction seems to be available for nma only.

I would appreciate your response.

[Xinqiu Yao]

Hi,

The function nma() includes ANM (See help(nma.pdb) and the explanation for the argument ff). aanma() is an elastic network model based on all heavy atoms. It is not ANM.

Hope it will help.

[Mamta Mohan]

Thank you. Yes, it does help.

I realized nma() does contain ANM and other ff's. I will read related documents for more explanation.

I will let you know if there is any issue.