The “oh shit” moment came when I started running a short DPPC run on trusty gromacs 4.6 with CHARMM36. The bilayer switched from liquid crystalline to gel phase and I knew I was in trouble. Played with the system size, increased the temperature from 323 to 333K – no luck. Turns out there is some pretty strong sensitivity of the lipid properties to electrostatics treatment in gromacs.

The key paper is probably Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study (paywall) which demonstrates the sensitivity to electrostatic parameters and proposes some solutions.

The gromacs authors have suggested their own parameters for running CHARMM with gromacs.

The topic has attracted a lot of attention on the gromacs mailing list, two useful threads are below:

  • https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083370.html
  • https://www.mail-archive.com/gmx-users@gromacs.org/msg64050.html