[gmx-users] g_helix

[Carla Jamous]

Hi everyone,

Please I need some advice concerning g_helix:

It's the first time I use this analysis. In the manual, it says:
g helix computes all kind of helix properties. First, *the peptide is
checked to find the longest helical part.*
This is determined by Hydrogen bonds and Phi/Psi angles. That bit is fitted
to an ideal helix around the
Z-axis and centered around the origin. Then the following properties are
computed:

However, when I do the following:

g_helix -s topol.tpr -f traj.xtc -n index.ndx -cz x.gro -co y.gro

I can't see anywhere if the program tells me which part is the longest
helical part. And I don't understand what are x.gro & y.gro

Please can anyone tell me more about this option, because it's not very
clear in the manual.

Thanks

Carla
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