15-residue triosephosphate isomerase peptide was subjected to 50 ns molecular dynamics in order to investigate its free energy that the peptide visited throughout the simulation (3D plot). The conformation with minimal free energy (deepest valley) was detected at timestamp of 19290 with an Rg value of 0.75 nm and an RMSD value of 0.5 nm, respectively.
Normal approach is to find a 2D or 3D subspace eg by principal components analysis. pcasuite (here: http://mmb.pcb.ub.edu/software/pcasuite/ ) is one of many tools that will do the job. If you have good sampling you can construct a potential of mean force on the subspace [ G = -kT ln(P(x)) ]. Probably your sampling isn't good enough to do this, so instead you will have to read into the subject and consider something more advanced, sorry, or else run for longer.....
- Badges
- Science topic
- Similar topics
- Chemistry
- Theoretical Chemistry
- Computational Chemistry
- Molecular Dynamics