Quoting Kirill Bessonov <[email protected]>: > 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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [email protected] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
