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

Chris Neale chris.neale at utoronto.ca
Sun Aug 12 20:55:24 CEST 2007

>Yesterday 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.

1. There is a delay between your posting and the appearance of your question on the mailing list.
Don't post multiple times to the mailing list. It will only reduce your chances of getting a reply.

2. Don't post separately to a particular user. It will only reduce your chances of getting a reply.

3. Search the archives. Had you done that, you would already have your answer.That answer is:
a) use double precision for energy minimization
b) start md. The acid test of a minimization is your ability to run md without crashing.

Look at your strating structure using VMD. in the middle vertically is a row of 4 tabs. Use the one on the right and
turn on the periodicity. Does it look as you expected?

You mention that you got a lipid monolayer but you said that you wanted a bilayer. This could be the reason you got
high energy.


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