I need to create a DOPC bilayer and need to change it’s area per lipid value in constant temperature settings. To do this, I plan to laterally compress the bilayer. Is there a method to compress a bilayer laterally in GROMACs and if so, how?
Use semi-isotropic pressure coupling with a sufficiently high pressure in x/y.
Thank you. 1 small question. Should I keep the compressibility in x/y the default value or should I specify a value specific to DPPC since I am applying a pressure in x/y plane?
I think you should be able to keep it at the usual water value. The hydrostatic pressure is dominated by the water as there is much more of that an the compressibility is much lower. But when scaling x/y and z independently while keeping the volume roughly constant, the compressibility will be different. Anyhow, if the compressibility is too low, the only effect is that the pressure scaling with be slower than tau_p, which is never an issue in practice.
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Thank you very much. this resolved my issue.
Hi Hess,
Now, that I am applying pressure in x/y direction, in my NPT equilibration steps, the box dimension x and y keeps shrinking, which I think means the system is not equilibrated. So, should I keep increaseing NPT equilibration time until it reaches a stable area for the applied pressure? Currently I have equilibrated to 12 ns.