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
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