Optimal MDanalysis.transformations for correcting PBC?

[Sanjiv Kumar]

Hi, 

I am new to MD simulations and still trying to figure out both MDAnalysis and LiPyphilic.

I ran an MD with a peptide in presence of POPG and POPE, the system was built using CHARMM-GUI with box-type HEXAGONAL, ran MD with Gromacs (2021.3). Doing analysis using MDAnalysis(v2.0.2) and lipyphilic (v0.10.0) on Ubuntu (20.04).

I am trying to perform MDanalysis.transformations for correcting periodic boundary conditions (PBC) as suggested previously in the forum discussion, user guide and suggestions by Paul from LiPyphilic.

Created a reference structure of centered protein:

`import MDAnalysis as mda

import MDanalysis.transformations as trans 

u = mda.Universe(tpr, trr) 

protein = u.select_atoms("protein") 

non_protein = u.select_atoms("not protein") 

transforms = [ trans.unwrap(protein), trans.center_in_box(protein, wrap=True), trans.wrap(non_protein), ] 

u.trajectory.add_transformations(*transforms) protein.write("reference-protein-structure.pdb")`

and re-loaded the original universe for rotation and transformation:

`import MDAnalysis as mda 

import MDanalysis.transformations as trans 

ref_u = mda.Universe("reference-protein-structure.pdb") 

u = mda.Universe(tpr, trr) 

protein = u.select_atoms("protein") 

transforms = [ trans.unwrap(non_protein), trans.fit_rot_trans(protein, ref_u, plane="xy", weights="mass") ] 

u.trajectory.add_transformations(*transforms)`

The lipid membrane is not breaking when I visualize trajectory in comparison to previous other sequences of transformations I tried, BUT the overall structure of the system (peptide and lipids) looks stretched as if PBC's are not applied, and peptide jumps around, image attached.

What is the right way to do this? What am I doing wrong and what can I do to correct it, so that the trajectory looks normal?

Please help.

With regards, 

Sanjiv Kumar