[gmx-users] End-to-End Vector Relaxation Time

atanu das samrucu at yahoo.co.in
Mon Jul 20 18:52:08 CEST 2015

Hi All,
I have a 1 micro-second trajectory of a 11-residue peptide in explicit solvent. I want to calculate the end-to-end vector relaxation time for the peptide segment. Now, during post-processing the raw trajectory file, I ran the following commands ----
1. trjconv -s md.tpr -f md.trr -o md-pbc.xtc -pbc nojump (pbc correction)
2. trjconv -s md.tpr -f md-pbc.xtc -o final.xtc -fit rot+trans (fit molecule to the reference structure) 
If I calculate the end-to-end vector relaxation time from the trajectory final.xtc would I get the correct result or I need to calculate the vector relaxation time without removing rotational and translational motions i.e.  trajectory after pbc correction?     

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