[gmx-users] How to maintain the same exact positions of the protein and ligand in the extracted frame/pdb file as they were in the trajectory form?

[Wayne Chen]

Hi,

I'm a student at National Taiwan University doing research on protein-ligand
interactions using MD simulations with GROMACS (version 4.5.3). In our
simulations, we placed a protein (group A) and a ligand (group B) in a box
under periodic boundary condition and ran for 20ns.

I am trying to obtain snapshots of specific time frames within the
trajectory file I got, but I am running into trouble outputting the exact
position of the protein relative to the ligand when converting the frames
into pdb files. Because of the period boundary condition, a snapshot may
have the protein located on one side of the box and the ligand on the
opposite end, but their actual relative positions---as measured by center of
mass (COM) between specific region within the protein and the COM of the
ligand----are in fact much closer to each other (1.33nm as calculated by
GROMACS as part of the trajectory vs. 7.585nm after being converted into a
pdb file).

So my question is: How do I maintain the same exact positions of the protein
and ligand in the extracted frame/pdb file as they were in the trajectory
form?

Thank you very much
                                                                                                                                    
Wayne Chen 

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