Tutorial Abl-SH3:p41 example, 5th step, PolarTheta PMF calculation, delta G not equal to 0

[Jiasheng321]

Congratulations on your great work and paper!

I am following the 2022 BFEE2 Nature protocol paper, to learn calculating the absolute free energy of the Abl-SH3:p41 tutorial example in the geometrical route. At each step I updated the colvars centers for EularTheta, EularPhi, and EularPsi in the colvars_*.in files. At the 5th step of PolarTheta, I could not find an optimal value of PolarTheta, which would correspond to deltaG= 0. The lowest deltaG value in the pseudo-quadratic curve of abf_1.abf1.czar.pmf of the PMF calculation that I could get was 1.026 Kcal/mol corresponding to 127.5 degree of PolarTheta. Also I noticed that the simulation or the PMF calculation seemed to be not converged, as there was not an approximate plateau of the time evolution of the PMF RMSD, based on the PMF convergence calculation plot of abf_1.abf1.hist.czar.pmf. The main running parameters were 115-135 degree for lowboundary and highboundary of PolarTheta, 5000000 steps (10 ns), one windows or strata, timesteps 2 fs, fullelectfrequency 1.

What should I do next? Do I need to repeat the simulation calculation one more time, because of the chaotic nature of MD of different runs? or Do I need to enlarge the angle search range of 115-135 degree for lowboundary and highboundary of PolarTheta ? or should I proceed with this non-zero deltaG for subsequent steps of free binding energy calculation, such as 006_PolarPhi, 007_r, and 008_RMSDUnbound? Thanks very much.

Sincerely,
Jiasheng

[Jiasheng321]

The main running parameters were 117-137 degree for lowboundary and highboundary of PolarTheta, 5000000 steps (10 ns), one windows or strata, timesteps 1 fs, fullelectfrequency 1. The delta G = 1.1488 Kcal/mol, corresponding to 126 degree of PolarTheta.

[Jiasheng321]

According to the text in the 2022 BFEE2 Nature protocol paper and Figure 8 in it, the delata G corresponding to the optimal PolarTheta seemingly should be zero, but my result is not that case， or is not like that. Thanks.