GROMACS version:5.1.4
GROMACS modification: No
How can I calculate time dependent configurational entropy of a protein along full trajectory?
I have used the following command:
#Covariance Analysis
gmx covar -f file_name.trr -s production.gro -o eig_heav_atom.xvg -v eig_heav_atom.trr -ascii eig_heav_atom.dat
#eigenvector analysis
gmx anaeig -f file_name.trr -v eig_heav_atom.trr -entropy -temp 300K -s production.gro -n protein.ndx -comp eig_comp.xvg -b 0 -e 2000
But I got the following results…
The Entropy due to the Schlitter formula is NaN J/mol K
The Entropy due to the Quasi Harmonic approximation is 19252.4 J/mol K
Please help me so that I can get the entropy value for Schlitter’s formula.
Thank you
Rabiul Gazi
email: 519cy1029@nitrkl.ac.in
Department of Chemistry, NIT Rourkel
India