Wrap keeping residues whole but forcing specific atoms to be in unit cell

[pcharchar]

Hi all,

As the title implies, is there a way to wrap a trajectory, but ensure specific atoms are in the unit cell during the wrapping process?

For context, what I want is to wrap an all-atom bilayer trajectory where all phosphorous atoms are in the unit cell, but lipids (residues) are kept whole and will have some atoms (but not P) protrude if they are near the boundaries.

I was thinking to make a custom, on-the-fly transformation, that conceptually would:
1 . save original P positions to variable
2. wrap P atoms to unit cell
3. make translation vectors for each P atom, based on how much they moved
4. reset P positions to origin
5. apply the translation vectors to the atoms in each residue

This seems cumbersome, especially if something already exists?

Also, I have cardiolipin with two P atoms per residue... so have to think of a clever way to only break those residues if one P atom crosses PBC.

A similar command in VMD, (just not for cardiolipin), would be:
pbc wrap -compoundref "name "P.*"" -compound residue

Thanks for the advice,

Patrick

[orbeckst]

A custom transformation is probably your best bet. AtomGroup.unwrap() has some flexibility but perhaps not enough for what you need. Maybe you need unwraps for different specific groups. It will likely be slow.

[pcharchar]

Thanks Oliver - I'll find a workaround.