[lammps-users] Re: Covariance matrix

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1

Hi,

Does anyone know of a good way to calculate the covariance matrix from LAMMPS data? Is there a way to do this in LAMMPS? If not, what open source tools do people use to do this?

I’m trying to do principal component analysis (PCA, also known as quasi-harmonic analysis), and need to calculate the fluctuation matrix / covariance matrix.

Any help pointing me to good open source solutions to this problem would be appreciated.

Thank you very much for taking the time to read this.

Ella Gale

Stressed-out Ph.D student.

2

Hi Ella. You can do quasi-harmonic analysis with
CHARMM. I'd recommend converting the LAMMPS dump files
you've made into a CHARMM trajectory using the mkdcd
fortran codes included in the LAMMPS package tools
directory. Then use CHARMM to do the analysis. I hope
this helps! -Paul