[gmx-users] how to reimage PBC based on distance to a given selection without recentering or otherwise changing atomic coordinates

Mark Abraham mark.j.abraham at gmail.com
Sat Feb 4 13:28:06 CET 2017


I've never really use it myself, but I imagine trjconv -pbc cluster is
useful for this kind of scenario when you want to treat a group of
molecules as indivisible.


On Sat, 4 Feb 2017 09:33 Christopher Neale <chris.neale at alum.utoronto.ca>

> Dear users:
> I have a system in which molecule A is in direct contact with molecule B.
> However, molecule B is imaged in a different periodic cell. What I would
> like to do is to get an image of both molecules in a periodic
> representation in which they actually are in contact (i.e., reimage
> molecule B such that it is closest to molecule A). However, I do not want
> to lose spatial information with e.g. a trjconv -center -pbc mol command.
> This is part of a complex automated build procedure and I can get into
> more details if that is useful, but the crux is that I am extracting a
> frame from a simulation, building more atoms onto molecule A, and setting
> up a new simulation. To build onto molecule A, I want to then do a vacuum
> EM before adding it back to the water box, for which I first enlarge the
> vacuum box, and changing box dimensions is messing with the periodicity and
> throwing molecule B away from molecule A in an unrealistic fashion
> (molecule B is a tightly bound ligand).
> I could do what I want by breaking each molecule out into its own box,
> checking for contacts, reimaging, and then putting them back together. I
> presume (but have not checked) that I could also do this by making a new
> .itp file in which both molecule A and B are part of the same [ molecule ]
> definition and then running a zero-step mdrun. However, I am writing to see
> if anybody knows how reimage based on a selection (would be a single atom
> in molecule A near the contact between molecule A and B) more elegantly
> with processing tools available in gromacs.
> Thank you for your help,
> Chris.
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