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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