[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

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

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