[gmx-users] Decreased Area Per Lipid for Lipid Bilayer obtained from CHARMM-GUI

[Nidhin Thomas]

Hello GROMACS Users,

I have modelled a mixed bilayer system consisting of 35 DPPC lipids and one POPA lipid (in each monolayers) using CHARMM-GUI. NPT ensemble was chosen while creating the model. TIP3 water model was used for modeling. I did not use surface tension for the membrane.

I have simulated the system for 50 nanoseconds now. I have noticed that average area per lipid of the system is only 58.55 Angstrom2. I saw from literature that it should be around 63 and even at CHARMM-GUI, it is mentioned as 63 while creating the bilayer.

I have used the exact .mdp files given by CHARMM-GUI for minimization, equilibration and production run.

Can anyone please help me identify what could have possibly gone wrong in my simulation? I have attached the .mdp file used for production run and equilibration here for reference.

In addition, I keep on getting these NOTES while running the grompp command prior to mdrun before it creates a .tpr file. I don’t know if this has got something to do with the simulation.

NOTE 1 [file step7_production_2.mdp]:
  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1

Estimate for the relative computational load of the PME mesh part: 0.05
Excluding 2 bonded neighbours molecule type 'TIP3'

There was 1 note
Excluding 1 bonded neighbours molecule type 'POT'
Removing all charge groups because cutoff-scheme=Verlet
Setting the LD random seed to 2417118902
Estimate for the relative computational load of the PME mesh part: 0.05

There was 1 note
Removing all charge groups because cutoff-scheme=Verlet

Thanks a lot for the help!

Nidhin Thomas