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. Thanks, Parul Tewatia
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