[gmx-users] construct lipid bilayer from single lipid (fwd)
David van der Spoel
spoel at xray.bmc.uu.se
Sun Aug 12 12:06:39 CEST 2007
---------- Forwarded message ----------
Date: Sat, 11 Aug 2007 20:12:28 +0800
From: Q733 <sansanqin00 at mails.tsinghua.edu.cn>
To: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: construct lipid bilayer from single lipid
Dear Professor Spoel:
I have read your steps on how to construct a lipid bilayer from a single lipid in the mailing list and I want to repeat it .But I met with some problem,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 getting 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. I tried to post this message in the mailing list ,but it didn't appear on the net, I just didn't know why.
Will you kindly give me some suggestion?
Thanks very much
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