Be careful when you draw conclusions from your results though. I
suggest that you start two simulations from different coordinates and
look at their convergence. In my hands, this type of thing can take >>
1 us to converge, and that's without any major conformational changes
in the peptide...
Chris.
Quoting Kirill Bessonov <kbessonov at gmail.com>:
Dear gromacs pros,
I need to calculate depth of DMPC bilayer penetration by my 14 aa long
peptide. I'm not sure how to do it, but I have tried g_dist program and
calculated distance between DMPC and peptide groups for every frame of
simulation. Is that correct way of doing it or maybe there is a better
way? I've got xvg file. First column is time and second is distance in
Amstrongs?
If you want the "depth" distance, you could then calculate the
distance between
the center of the DMPC bilayer and a suitable reference (phosphate?) and take
the difference. But essentially, you have what you want already, just from a
different perspective.
Distances in Gromacs are always printed in nm, per the manual, and the
header of
the .xvg file.
-Justin
Thank you
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