[gmx-users] gmx distance

Alex nedomacho at gmail.com
Tue Aug 4 00:19:30 CEST 2015

v. 5.0.5
I need to calculate the distance between COMs of two groups (both in index
file) as a function of time. I can't think of anything simpler.
 I'm doing:
"gmx distance -f traj.trr -n index.ndx -oav dist.xvg" and then selecting my
groups manually from the menu.

 I am getting:

"Selection 'DG' does not evaluate into an even number of positions (there
33 positions)"

To this effect, the manual states something that could have easily come out
of Donald Trump:

"gmx distance calculates distances between pairs of positions as a function
of time. Each selection specifies an independent set of distances to
calculate. Each selection should consist of pairs of positions, and the
distances are computed between positions 1-2, 3-4, etc."

It is my understanding that the distance is calculated not as the distance
between COMs (which is only one pair), but something else. I want the
distance between the COM of my DG and one other group.

Anything I am missing in the supplied options?



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