[gmx-users] Protein pore collapse during simulation.

[Yogesh Sharma]

Hi
I have used inflategro to pack protein in lipid bilayer. While simulation
run protein channel is getting collapsed. can i get some suggestions, if it
is because of the wrong orientation of my protein in bilayer or lesser area
per lipid after shrinking iterations? i have used charmm assembly as
control, where protein channel is fine throughout trajectory. for
inflategro packing i have used 128POPC fom calgiary university website.

I reached an area of 0.67 nm2 while area in upper leaflet was 0.71 and in
lowerleaflet it was 0.70nm2.

  *thanks for your feedback and valuable time*