[gmx-users] how to do dPCA?

Seera Suryanarayana palusoori at gmail.com
Tue Oct 17 07:04:11 CEST 2017

Dear gromacs users

I would like to do dPCA for my 100ns trajectory. When see in the gromacs
tutorial I could not create the covar.ndx file. My peptide is 20 residues
length. I made .ndx file for dihedral angles and after generating the
dangle.trr file. But here I have one problem, to generate the .gro file we
have to create the covar.ndx file based on the 2*N/3 formula. As my peptide
has 20 dihedral angles, the covar.ndx file will have 14 atoms. But I want
to generate .gro file to my complete peptide (20 residues). I request you
to here help me out.

Thanks in advance
Graduate student

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