NAMD trajectory files

[MamtaMohan]

Hi,

I was wondering if TAMKIN can process NAMD files. I am interested to use TAMKIN for Normal Mode Analysis.

I will appreciate your response.

Mamta

[tovrstra]

@MamtaMohan : Trajectory files cannot be used as an input for a Normal Mode Analysis (NMA). You need a Hessian calculation as input. This is the matrix of second order derivatives of the energy w.r.t. displacements of the atoms in Cartesian coordinates, at a single geometry. Given this Hessian matrix, TAMkin can do different types of NMA analyses. (Most codes that can generate a Hessian can also do one basic type of NMA.) Trajectory files cannot be used in TAMkin and these would rather be used for PCA analysis, which TAMkin does not do. I've browsed through the NAMD documentation but it seems that it does not offer an option or flag to calculate the Hessian matrix.

[MamtaMohan]

Dear Toon,

Thank you for your response.

I have resolved issue regarding NAMD input to Tamkin.

I would request you not to pursue this.

I will write to you if there are any questions in future about Tamkin.

I truly appreciate your help.

Mamta