GROMACS version:
GROMACS modification: Yes/No
I have 2 proteins and I have performed 10 ns trajectory for each protein ( 3 replicates each). i want to do a PCA analysis and identify the difference between the 2 proteins. should I do PCA for all the replicates seperately or should merge the 3 replicates into a single trajectory?
You should pool the replicates and perform the analysis on the whole ensemble. I will caution that 10 ns is not nearly enough data to even reach reasonable sampling to perform PCA.
thankyou @jalemkul . I have merged the trajectory of replicates using trajconv. I have a question what .tpr file should I use with the merged trajectory for PCA. Is there a way to merge .tpr files also?
You typically use a single .tpr (GROMACS binary input file) file for the analysis. The .tpr file contains information about the molecular topology, force field parameters, and simulation parameters. When you merge trajectories, you are combining the trajectory files, not the .tpr files. However, it’s important to note that if you use only the protein part of the trajectory, you may need to update the .tpr file accordingly