[gmx-users] breaking lipid A tail in minimization

Karim Mahnam 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
itp file)
Thank you very much
Karim Mahnam, Associate professor of shahrkord university, Iran

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