[gmx-users] Dihedral PCA

[bharat gupta]

---------- Forwarded message ----------
From: bharat gupta <bharat.85.monu at gmail.com>
Date: Thu, Nov 21, 2013 at 4:52 PM
Subject: Re: Dihedral PCA
To: Discussion list for GROMACS users <gmx-users at gromacs.org>


Hi,

I want to perform the dihedral PCA for two residues of a turn region in a
protein i.e 4 dihedral angles. I have created an index file for the atoms
constituting phi and psi angles for those two residues. But I don't
understand what has to be written in covar file .. According to manual it
says "covar.ndx, which necessarily contains one group of atom 1 to
integer(2*N/3), where N is the number of dihedral angles". I don't get the
meaning of this line ?? Can anybody guide me ...

Regards
----------------------
Bharat