[gmx-users] Flip a bilayer
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.
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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