Recognize Drude particles, improve handling of lone pairs

Amber-MD / cpptraj

Biomolecular simulation trajectory/data analysis.

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Recognize Drude particles, improve handling of lone pairs #1099

Closed drroe closed 3 months ago

drroe commented 3 months ago

Version 6.29.0.

Drude particles are now identified from Charmm PSF files and given the element type DR.
The lone pairs section is now properly read from Charmm PSF files.
The distance, angle, dihedral, and vector actions now check if the total mass of atoms in a mask is zero when center of mass is requested; this can happen when e.g. only lone pairs are selected.
Add the geom keyword to vector to enable vector calculation using geometric centers instead of center of mass (to get around the aforementioned zero mass problem).
Add the debye keyword to vector dipole to report dipole vector in units of Debye.
Lone pairs are given different (shorted) default distances when no bond parameters are present.
Add the bondparm command for printing the bond parameter table.

Adds a test for reading Charmm PSF files with Drude particles. Updates the manual.

drroe commented 3 months ago

Grr, python 😠 @hainm can you take a look? https://github.com/Amber-MD/cpptraj/actions/runs/10618137181/job/29432643446?pr=1099

I'm going to merge this stuff if everything else passes this seems like one of those "with some python versions it works, with some it fails" errors, i.e. the errors are not related to the changes in this PR.

hainm commented 3 months ago

I will have a look next week, I will have an international flight.

Hai

On Thu, Aug 29, 2024 at 10:50 PM Daniel R. Roe @.***> wrote:

Grr, python 😠 @hainm https://github.com/hainm can you take a look? https://github.com/Amber-MD/cpptraj/actions/runs/10618137181/job/29432643446?pr=1099

I'm going to merge this stuff if everything else passes this seems like one of those "with some python versions it works, with some it fails" errors, i.e. the errors are not related to the changes in this PR.

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hainm commented 2 months ago

Grr, python 😠 @hainm can you take a look? https://github.com/Amber-MD/cpptraj/actions/runs/10618137181/job/29432643446?pr=1099

I'm going to merge this stuff if everything else passes this seems like one of those "with some python versions it works, with some it fails" errors, i.e. the errors are not related to the changes in this PR.

@drroe It seems like a real issue instead of python thing. um. I don't know why yet.

drroe commented 2 months ago

@hainm looks like the problem is pytraj isn't fully compatible with numpy 2.1.0. When I pin numpy to 2.0.0 the tests pass again (see https://github.com/Amber-MD/cpptraj/pull/1102).

hainm commented 2 months ago

@hainm looks like the problem is pytraj isn't fully compatible with numpy 2.1.0. When I pin numpy to 2.0.0 the tests pass again (see #1102).

yay. thanks for resolving this in cpptraj. I will think about a solution for numpy 2.1.0. I think it's because of Cython version that generates the c++ files.