Metadynamics tutorial

HADDOCK
1

I am working on the updated version of the metadynamics tutorial, to be found here: Tutorial EDES / HADDOCK for ligand-protein docking – Bonvin Lab

Some files are missing in the updated version, like e.g., plumed.2.dat and plumed.3.dat are missing and plumed-common.dat contains only descriptions related to cv1 and cv2.
Is it possible to add the missing files?

2

Hi olivierb,
I’m Andrea Basciu, the guy who set up the tutorials.

Not sure if I understood your question correctly but at the link you are sharing, you will find an older version of the tutorial, and not the updated one.
In the older version, indeed, all the needed files (including plumed.2.dat, etc.) are in the folder you can download. So, for that one, there shouldn’t be any problem concerning the availability of the files.

In the updated version (available here), on the other hand, yes, the files you name are missing and/or incomplete. The reason for that is that the user was requested to make those files. For example, at the end of part 2 of the updated tutorial (available here), you will see a sentence in bold asking the user to complete the file plumed-common.dat. The same goes for the other files. If you follow the instructions in the tutorial, you should be able to make those files. The tutorial was thought indeed with the aim to guide the user towards all the steps.

The two tutorials (older and newer version) cover the same topic but they are a little bit different in certain aspects, so it’s better not to mix them up. Either you follow one or the other. The main ideas will be exactly the same, but the specific commands / procedure is presented in a slightly different way in the two tutorials.

Hope it helps.
In case of any other doubt, please let me know

Best regards,

Andrea

3

Hi Andrea,

Thanks for the detailed answer.
Regarding the older version, I really don’t see the indicated missing files. I attach a list of the files in the plumed folder to this mai.

But that doesn’t matter anymore for me. Since there is an updated version, I will use this one from now on.

Best regards,

Olivier