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.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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