Action for reading masses and charges from a PDB file

gtribello commented 2 weeks ago

Description

While creating all the stuff for the test centre I realised that some codes (I-Pi) don't have any mechanism for passing masses and charges of atoms to PLUMED. Furthermore, I'm told it would be difficult to add the code to pass masses and charges to PLUMED using these codes. I thus created this action that allows you to set the values of the masses and charges from the PLUMED input. To set the masses and charges you just give the action a PDB file with the masses and charges in the beta and occupancy columns in the usual way.

Target release

I would like my code to appear in release 2.10

Type of contribution

[x] changes to code or doc authored by PLUMED developers, or additions of code in the core or within the default modules
[ ] changes to a module not authored by you
[ ] new module contribution or edit of a module authored by you

Copyright

[x] I agree to transfer the copyright of the code I have written to the PLUMED developers or to the author of the code I am modifying.

[ ] the module I added or modified contains a COPYRIGHT file with the correct license information. Code should be released under an open source license. I also used the command cd src && ./header.sh mymodulename in order to make sure the headers of the module are correct.

Tests

[x] I added a new regtest or modified an existing regtest to validate my changes.
[x] I verified that all regtests are passed successfully on GitHub Actions.

GiovanniBussi commented 2 weeks ago

@gtribello I think this is useful, but I would not use PDB format. In PLUMED we only use PDBs when we have to provide coordinates (for RMSD) or names / residues (for MOLINFO). Here it's just reading a vector, I would save the user from the potential issues with misformatted files.

Why not using the same format that you can now write (with DUMPMASSCHARGE) and read (with driver --mcfile)?

In addition, I would call the action READMASSCHARGE for consistency.

If you like the PDB, we can add the option of writing a PDB with charges in DUMPMASSCHARGE and reading it in READMASSCHARGE, but I am not sure it is a good idea.

gtribello commented 2 weeks ago

Thanks for these comments @GiovanniBussi. I have changed the name as you suggest now and have also added the option to read either a pdb file or the mass charge file. This is the same as what we allow with driver so I think it makes more sense.

Thanks again.

GiovanniBussi commented 2 weeks ago

This is the same as what we allow with driver True, I didn't remember this... Thanks!

plumed / plumed2