[gmx-users] Methodology of dPCA

Seera Suryanarayana palusoori at gmail.com
Wed Jun 13 10:41:20 CEST 2018

 Dear gromacs users,

I am Surya a Ph.D. scholar from lab of computational biology,  CDFD,
Hyderabad.  I have done simulations for 100ns of 20 residue length peptide.
I have done dPCA as mentioned in the gromacs tutorial. I have made a
dangle.ndx file with all dihedral angles atom numbers. I created .trr file
with 24 atoms of every time frame. Then based on the formula 2*N/3, I made
another .ndx file of 24 atom numbers as my number of dihedral angles are 36
to create resized.gro file.  Kindly tell me whether my methodology is
correct to go ahead for further analysis such as gmx covar and gmx anaeig.

Thanks in advance
Graduate student

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