I use PMX to calculate when Ser mutates into Phe, when calculating ΔG in water, the repeatability is very poor, I use the version of gromacs2020.7.
In addition, I would like to ask if the trajectory file generated after using pmx can be used to analyze RMSD, RMSF and the number of hydrogen bonds? Because when I use pymol to view the mutation site, the key display of the mutation site is wrong, what should I do about this situation?
What exactly do you mean with “poor repeatability”? What is the standard error that you get from multiple repeats? Is each individual simulation sufficiently converged?
Hybrid structures contain residues that can represent WT and Mut states. For A-state, you can just hide the dummies. For B-state, you would need to map the atoms to those of an actual structure in the B-state. If you omit the mutated residue, the rest of the structure follows the standard atom naming
From these 5 runs I see that the standard error of the mean is ~2.5 kJ/mol which seems reasonable. Only water3 appears to be somewhat of an outlier. You could check visually if you spot anything different happening in that trajectory. Also, how long are your transitions?
Yes, I tried to generate RMSD using a tpr file without error, but I found that using tp and using a gro file to generate RMSD was very different. My input file GRO is after the recovery track, while the TPR file is the original file that was generated, I will search for the cause of the problem.