[gmx-users] construct lipid bilayer from a single lipid

Shanshan Qin sansanqin00 at mails.tsinghua.edu.cn
Sun Aug 12 04:53:21 CEST 2007

Hello, gmx-users.Today I tried to construct a lipid bilayer through a single lipid. The process is like this:
1. editconf -f lipid.pdb -princ -c -box 0.8 0.8 3.0  -o lipid.gro
2. genconf -f lipid.gro -nbox 4 4 1 -o box.gro
3. modified vanderwals radii in the vanradii.dat in the top folder ,changed the C value to 0.3
4. editconf -f box.gro -box 3.2 3.2 4.5 -o box1.gro
5. genbox -cp box1.gro -cs -o mix.gro
after these steps ,I got a lipid monolayer and water monolayer got together ,without water in the lipid hydrophobic tails.However when I ran energy minimization steps, it converged to the precision of computer after only 16 steps and still have very high energy. How can I make the starting configuration energy lower?
By the way ,I have tried both steep and cg method, neither worked well.Any suggestion will be appreciated, thanks.
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