[gmx-users] applying surface tension to a membrane bilayer

凌未风 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. 


Ruo-Xu Gu,

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