[gmx-users] Flip a bilayer

Justin Lemkul jalemkul at vt.edu
Fri Feb 16 13:52:48 CET 2018

On 2/15/18 12:38 PM, Poncho Arvayo Zatarain wrote:
> Hello Gromacs users: I have a problem with a lipid bilayer, when i watch in vmd, is inverted, the water is in the middle and the lipid tails are outside. How can i flip it to a correct way? I´m trying with gmx trjconv -f file.gro -s file.tpr -n index -o file.gro -pbc whole but nothing happens. In index i use option System. What can i do to flip the bilayer? should i use lipid and water options in index?
Use the -trans option on the lipids to set a translation equal to half 
the box along the membrane normal.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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