GROMACS version: 2019.4
GROMACS modification: Yes/No
Hello GROMACS users,
As I simulated solvated complex system with a protein and a ligand involved, I’ve tried to calculate entropy difference along with trajectory.
As I searched how to calculate the entropy difference, I knew that eigenvector is needed. So I prompted gmx_mpi command as below:
1. gmx_mpi covar -s my_system.tpr -f my_traj.xtc -n index.ndx -o eigenval.xvg -v eigenvec.trr -ascii covar.dat -xpm covar.xpm -xpma covar.xpm
→ And select ‘Protein_LIG’ twice for group squares fit and covariance analysis
2. gmx_mpi anaeig -v eigenvec.trr -f my_traj.xtc -s my_system.tpr -n index.ndx -eig eigenval.xvg -3d 3dproj.gro -entropy -skip 100
→ And also select ‘Protein_LIG’ twice
But I can’t obtain entropy value what I want to estimate with the error message below:
2 eigenvectors selected for output: 1 2
Last frame 10 time 100.000
-------------------------------------------------------
Program: gmx anaeig, version 2020.2
Source file: src/gromacs/gmxana/gmx_anaeig.cpp (line 683)
Fatal error:
You have selected less than 3 eigenvectors
I can’t understand the error message… Is there anything what I’m missing?
Thank you for considering my question :)