[gmx-users] problem with lipid membrane

Parul tew parultew at gmail.com
Mon Sep 19 08:35:26 CEST 2011

Dear Gmx users,

I am working on a transmembrane protein and my system contains protein, DPPC

bilayer, water (spc) and ions. After adding ions I energy minimized the
system and used trjconv to remove periodicity.  In the equilibration phase
the lipid molecules were entering the voids in the solvent leaving the
protein naked. So, I used position restraint on the Z-plane and restrained the
phosphate head (atom 8) and one carbon atom on each tail (atoms 31, 50 with
a force constant of 1,000 kJ mol*-*1 nm*-*2.


; position restraint file for DPPC

[ position_restraints ]

;  i funct       fcx        fcy        fcz

   8    1       0       0       1000

  31    1       0       0       1000

  50    1       0       0       1000


But after running a simulated annealing for 500ps I get a distorted lipid
membrane where the lipids tend to pack at one end but open at the other end
of the box.

After this I had put position restraint on all the atoms of the lipid on the
z-plane and again tried the simulated annealing but it gave the same result.

I am not able to understand where I am going wrong.


Parul Tewatia
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110919/39622e99/attachment.html>

More information about the gromacs.org_gmx-users mailing list