[gmx-users] Depth of penetration of DMPC lipid bilayer. How?

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Dec 23 21:52:25 CET 2009

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...


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.


> Thank you

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