[gmx-users] Semiisotropic pressure coupling & comm_grps (VCM)

[Alok]

Dear All,

I have two basic questions regarding membrane protein simulation. First regarding Semiisotropic pressure coupling (NPAT) and second regarding comm_grpp (VCM).

1) If I want to use NPAT ensemble (x/y dimensions of bilayer to be fixed) then is following the correct way to define?

Pcoupl                   =  Berendsen
Pcoupltype            =  semiisotropic
tau_p                     =   2.0     2.0 
compressibility     =   0        4.5e-5
ref_p                     =  1.0      1.0

2) I want to remove center of mass translation so in following which one is better?

    a)    comm_mode                =  Linear
           nstcomm                       =  1
           comm_grps                  =  Protein_POP ; (both protein and lipid are together)

    b)    comm_mode                =  Linear
           nstcomm                       =  1
           comm_grps                  =  Protein POP ; (protein and lipid separately)



Thanks a lot

Best Regards,
Alok
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