[gmx-users] breaking lipid A tail in minimization
karimmahnam93 at gmail.com
Thu Jun 14 10:49:37 CEST 2018
Hello Dear GMX-users
I want to do MD simulation on Lipid A membrane bilayer via gromacs software
and G53A6 force filed.
I get lamp_final.itp and one_lamp.gro from "Lipidbook Package GROMOS-CKP
Gromacs Lipid A" site.
When I do steepest descent minimization with one Lipid A molecule in the
water box, everything is Ok. But when I do steepest descent minimization
with membrane contain 63 Lipid A (that I get from "
http://www.charmm-gui.org/?doc=input/membrane" site and removed
oligosaccharide heads) and 126 MG ions, it breaks lipid tail and hydrogen
bonds with carbons.
Would you please how can I solve this problem.
How can I make a pre-equilibrated bilayer Lipid A structure for G53A6
I attached topology file to this mail. (I changed only atom names in itp
file according to Charmm27 force field, because charmm-gui make bilayer
with Charmm27 atom name and as you know atom names are not important in
Thank you very much
Karim Mahnam, Associate professor of shahrkord university, Iran
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