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

Hi Kirill, Although I can't directly address your question, I came across some recent work dealing with depth of penetration in lipid bilayers. May be the authors could help you. http://www3.interscience.wiley.com/journal/122351396/abstract

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

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.

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

Quoting Kirill Bessonov : > 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

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

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 b