[gmx-users] Problems in simulating the ion channels inserting into lipid bilayer

Xianhui Wu nanyu101 at sina.com
Thu Sep 11 07:27:01 CEST 2003

Dear gmx-users,
   I have tried to simulate how an ion channel inserts
into the lipid bilayer. And I have read the Dr.Tieleman's
paper about inserting of Alm,but he didnt tell us how
the Alm inserts into lipid bilayer such as DPPC.

   So,I tried to use Gromacs to simulate how the ion channel
inserts into lipid bilayer DPPC.I have tried to do as follows:

1. I have put the ion channle helix paralleled to the lipid bilayer.

2. I have add an external electric field along z direction, such as 0.33v/nm.

3. Run dynamics for 15ns

But when I run MD to 12nd ns, my box has changed in z direction, the z value 
became less and less and the x,y became larger and larger. And the P8 atoms 
moved to the the angle of the box, And the tails of DPP face the middle of 
the box, the ion channel is in the middle of box. The channel is in the 
middle of the box,but it did not insert into the lipid bilayer.Would you 
please give me some advices?Thanks a lot.

Best wishes,

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