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Feature #2860

Option for outputting min/max coordinates in gmx traj

Added by John Dupuis 9 months ago. Updated 9 months ago.

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Normal
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Description

It would be very useful to have a flag added (such as -maxcoord, -mincoord) to gmx traj to calculate the minimum and/or maximum coordinate of a group when analyzing the x/y/z positions of atoms in trajectories.

An example application would be measuring the minimum z-coordinate of a protein interacting with a membrane to determine penetration distance (relative to, e.g., average phospholipid phosphate z position)

There was some very minor talk on the email list I found: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-December/047660.html
And also a VMD solution given: https://www.researchgate.net/post/Gromacs_How_to_calculate_minimum_and_maximum_coordinates_of_the_system

It would be nice to have a basic feature like this implemented natively in Gromacs.

History

#1 Updated by Kevin Boyd 9 months ago

Hi,

For the functionality you describe, it's pretty easy to just e.g. calculate the z coordinate of the protein of choice, or of the phosphate coordinates, and subtract out the membrane COM (or center the trajectory on the membrane first).

More fundamentally, with periodic boundary conditions a minimum or maximum coordinate can be very misleading, even with an anchoring feature such as a membrane.

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