[gmx-users] I have not been able to do dPCA

Seera Suryanarayana palusoori at gmail.com
Tue May 1 07:04:09 CEST 2018

Dear gromacs users,

I would like to do dihedral PCA for my 20 residues trajectory. As I have
interested in first 10 residues of my peptide, I have generated the .ndx
file which has the dihedral atoms of first ten residues. Then I executed
the following command.

gmx_mpi angle -f  md_0_1.xtc -s md_0_1.tpr -n dangle.ndx -or dangle.trr
-type dihedral

Here I got the two output files. Among them, one is dangle.trr which has
only 14 atom positions with cos/sin. But I want ten residues atom positions
cos/sin. In other words, I need to get for first ten residues atom
positions cos/sin. I couldn't successful when I follow the dPCA tutorial on
the gromacs site.  Kindly tell me how to do it.

Thanks in advance
Graduate student

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