GROMACS version: 2018.5
GROMACS modification: Yes/No
I want to make a ‘energy vs reaction coordinate diagram’. I have three different conformations; A, B, and C. I have performed SAXS MD simulation as well as normal MD simulations.
I was thinking, I’d use gmx energy to get the free Gibbs energy, but I am at a loss at how to get a collective variable.
I’m thinking I could use those two as my x and y axes and plot the diagram. Is this possible? And how do I achieve collective variables?
I have also looked into using PCA, where gmx covar is used. However, I get the error
symtab get_symtab_handle 1065420047 not found
when I write
gmx covar -s waxsmd.tpr -f waxsmd-run.xtc -n index.ndx -o test.xvg -fit yes