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* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
