GROMACS modification: Yes/No
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Using GROMACS, we have simulated a lipid bilayer system comprising of 1024 DPPC. gromos53 a6 force field and Berger Lipid parameters are used as forcefields. The initial structure is taken from Tieleman’s website which contains 64 DPPC and then it was expanded in lateral direction using genconf command. After energy minimizing the structure using steepest descent algorithm, we first run NPT for 1ns for equilibration using Nose-Hoover thermostat and Parrinello-Rahman pressure coupling. Then, it was followed by a NVT run for 100ps using Berendsen thermostat. Then we run production run using NPT for 20ns. The temperature and pressure are set as 323 K and 1 bar.
We have calculated a few structural properties of DPPC lipid as given below,
- Area per lipid =60.72 angstrom square, which seems to be a little in the lower side using Berger-lipid parameters. We expected something around 62 angstrom square. As we are new in membrane simulation could anyone suggest whether 60.78 is acceptable with Berger lipid force field.
- From the Z- density plot, distance between head groups is calculated as 37.6 angstrom.
Any comment or suggestion over the acceptability of these values are welcome.