Procedure for WHAM calculations

[l.ca...@campus.unimib.it]

Dear Plumed users,

I tried to follow the umbrella sampling tutorial (https://plumed.github.io/doc-v2.5/user-doc/html/belfast-4.html). About wham analysis, in particular in the "combining multiple restraints" section, I read "An often misunderstood fact about WHAM is that data of the different trajectories can be mixed and it is not necessary to keep track of which restraint was used to produce every single frame".

After this step we have the entire concatenated trajectoty (alltraj.xtc) and the ALLCOLVAR files that will be used as input for the wham.sh script that compute histogram. It is not clear to me why the ALLCOLVAR files are used without specify which bias produces each frame.

In particular I obtained some strange low-energy point at the extreme of the grid (phi=-3.0) which I supposed is an artifact of this procedure.

In the GROMACS tutorial for umbrella sampling (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/01_pdb2gmx.html) this procedure (merging all the simulation and reweight all frames against all restraints) is not required.

Can you please explain me the reason of this particular procedure?

Thank you

Lara

[Gareth Tribello]

Dear Lara

If you read this paper the version of WHAM that is implemented in PLUMED is explained.

https://arxiv.org/abs/1812.08213

Gareth

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