Kinetics from metadynamics

[szlen...@gmail.com]

Hi all,


I hope someone can point me in the right direction here as I'm a bit confused. I'm working on getting the koff rate using the methods in https://doi.org/10.1073/pnas.1424461112,
coupled with the VES-Lugano-2017 kinetics tutorial scripts to see whether I can get a koff rate for my simulations. I've run into a problem with the time-reweighting.py script. I am following most of it until the conversion from energy in eV to kBT portion. The script is as follows -

kT=(2.479/298.0/96.485)*Temperature.

Now let's say for my system, is it possible to use this script and apply it to a ligand unbinding from a protein? The main question I have is that I'm struggling with what sort of a conversion (if any) I would need for my system. The kT, as spit out by plumed is 2.577483 kJ/mol (for a system simulated at 310 K). Is this the kT value that I would use? Is there any conversion needed there? Is it even okay to use this script for what I want? If I understand correctly, the kT needs to be a unitless value. I've changed all the other parameters to match up with my system and made sure all the columns match up correctly. Any help is greatly appreciated!


-Chris Szlenk

[ctsz...@yahoo.com]

I'll answer this one myself after reaching out to someone. The bias/kT will cancel the units out depending on what units you used. This can depend on simulation software. In my case, kT is 2.57 kJ/mol and the bias is also in kJ/mol, and so the bias/kT will cancel out so that I can take exp^(bias/kT). Only a conversion would be needed if units are different or you used different units. The tutorial used eV and wanted to convert to kJ/mol I believe which is why there are the conversions.

-Chris Szlenk