[gmx-users] Protein pore collapse during simulation.

[Yogesh Sharma]

sir,
 in efforts to find out the differences in the density of bilayers
generated by charmm and gromac(berger lipids) i used grid-mat. there are
significant differences in area per lipid.

with these settings for both systems:
override_vectors        5.2,10.0,6.9
grid                    20
conserve_ratio          yes
protein                 yes
precision               1.3
P_value                 5.0
#Lower Z limit: 3.036   Upper Z limit: 7.784

charmm with hydrogen (sq. A)
area per lipid upper leaflet: 10.5
area per lipid bottom leaflet 5.45

charmm (bilayer saved without hydrogen) (sq. A)
area per lipid upper leaflet: 13
area per lipid bottom leaflet 7

gromac (sq. A)
area per lipid upper leaflet: 70
area per lipid bottom leaflet 68
Are charmm values below experimental observation for POPC i.e gelation of
bilayer?