GROMACS version: 2021.1
GROMACS modification: No
These days, I am learning the analysis of production MD result, but I am confused about that which parts should be used for MD analysis, whole trajectory or balanced trajectory?
For example, the following RMSD figure.
If I want to do the clustering analysis, and do DSSP analysis, which part of the trajectory should be used for these analysis? The whole trajectory (0-300ns) or the balanced trajectory (200ns-300ns)?
I noticed that most of the gmx comands, they have -b and -e options, so I did the analysis only using -b 200 -e 300 -tu ns, which is the balanced part.
Can you help give suggestions if what I did is OK?