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<DIV><FONT size=2><FONT size=3>Yesterday I tried to construct a lipid bilayer
through a single lipid. The process is like this:<BR>1. editconf -f lipid.pdb
-princ -c -box 0.8 0.8 3.0 -o lipid.gro<BR>2. genconf -f lipid.gro -nbox 4 4 1
-o box.gro<BR>3. modified vanderwals radii in the vanradii.dat in the top folder
,changed the C value to 0.3<BR>4. editconf -f box.gro -box 3.2 3.2 4.5 -o
box1.gro<BR>5. genbox -cp box1.gro -cs -o mix.gro<BR>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?<BR>By the way ,I have
tried both steep and cg method, neither worked well.Any suggestion will be
appreciated.</FONT><BR><BR></FONT></DIV></BODY></HTML>