Showing posts from November, 2015

Feeling the burn: DPPC lipid CHARMM36 with gromacs

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: