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

[Christopher Neale]

In future posts, it is best to copy and paste your .mdp file because we can not all get attachments from the list.

Regarding your results, it is my understanding that the CHARMM-GUI has parameters for, and can build, many lipids systems whose parameters have not been completely validated by simulations in the literature (e.g. for things like APL). Last time I looked, PG was the only anionic charmm36 lipid that was shown to behave properly in bilayers (Klauda), though others may have since been shown to work well.

If the issue is not simply that the PA parameters are not very good, then one likely source of problem is that perhaps you are not using the NBfix ions? That could be a big deal. I never use Na with membranes for this reason, so you could try KCl instead.

Chris.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Nidhin Thomas <nidhin.thomas0624 at gmail.com>
Sent: 12 June 2016 18:38:43
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Decreased Area Per Lipid for Lipid Bilayer obtained        from CHARMM-GUI

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