How to Maintain the Integrity of a System Containing Multiple Independent Chains Across PBC in MDAnalysis

[erwusht]

Hi,

I'm currently working on a molecular dynamics simulation project that involves multiple protein chains within the same system. These chains are structurally independent (i.e., no covalent bonds between them) and occasionally span across the periodic boundary conditions (PBC), which complicates the analysis of their interactions and overall structure.

Is there a recommended approach within MDAnalysis to maintain the integrity of independent protein chains that may span PBCs?

Thank you in advance for your time and help!

Best regards,
Wu Shiauthie

[IAlibay]

@erwusht since this is more about usability than a bug, I am transferring this to our discussion forum in the hopes that someone may have a solution for you there.

[IAlibay]

@yuxuanzhuang I vaguely remember that you might have had some transformation to handle this somewhere? Would you be able to weigh in here?

[erwusht]

Thank you for helping me with my question.

[yuxuanzhuang]

Here is the code snippet I normally use:

# From https://groups.google.com/g/mdnalysis-discussion/c/umDpvbCmQiE/m/FKtNClazAwAJ
# Author: Richard Gowers

from MDAnalysis.transformations.base import TransformationBase
import numpy as np


class GroupHug(TransformationBase):
    def __init__(self, center, *others):
        super().__init__(max_threads=1, parallelizable=True)
        self.c = center
        self.o = others

    @staticmethod
    def calc_restoring_vec(ag1, ag2):
        box = ag1.dimensions[:3]
        dist = ag1.center_of_mass() - ag2.center_of_mass()

        return box * np.rint(dist / box)

    def _transform(self, ts):
        # loop over other atomgroups and shunt them into nearest image to
        # center
        for i in self.o:
            rvec = self.calc_restoring_vec(self.c, i)
            i.translate(+rvec)
        return ts
      

then you can group the protein chains together with e.g.

prot_chain_list = []

# group all the protein chains

for chain in u_prot.segments:
    prot_chain_list.append(chain.atoms)

prot_group = GroupHug(*prot_chain_list)
u.trajectory.add_transformations(
                        *[prot_group]
                    )

[erwusht]

Thank you very much for taking the time to provide the code and explain it to me.