[gmx-users] applying surface tension to a membrane bilayer
grx1985 at qq.com
Mon Mar 25 10:51:43 CET 2019
I am trying to apply a surface tension to a membrane bilayer, below is the mdp parameters I am using:
pcoupl = Berendsen
pcoupltype = surface-tension
tau_p = 10.0 10.0
ref_p = 500 1.0
compressibility = 4.5e-5 4.5e-5
I have two questions:
1, In the manual it is mentioned that compressibility should be accurate enough, I am wondering what is the recommend compressibility if I am trying to simulate a POPC bilayer.
2, In the manual, it is also mentioned that the compressibility of z direction can also be set to 0, so that one can get a constant height. If I use
compressibility = 4.5e-5 0
can I still get a physical correct ensemble (NPT)? How a constant height may affect the simulation system? I am running a membrane protein, and the main focus is the protein in my case.
I am thinking to use a constant height, because the force field I am using (charmm36) may result a mysterious sudden expansion of the bilayer in gromacs.
Thanks for your help, I really appreciate.
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