In CHARMM-GUI online server .mdp output file for equilibrium and production run has no pbc condition defined by default.
So here I have to add pbc condition manually to all .mdp file, or no need of pbc in membrane simulation with semiisotropic pressure coupling.
(I understand that pbc is required to eliminate the artificial boundary effect. )
my concern is that pbc is not included by default, if it's so important than why not included by default or there is some other reason.
The default value of the "pbc" keyword is "xyz," so periodicity is invoked by default. Your .log file from the run should confirm this.
Thank you Dr. Justin Lemkul. I found these lines in the log file
nstlist = 40
ns-type = Grid
pbc = xyz
periodic-molecules = FALSE
verlet-buffer-tolerance = 0.005
Good, that confirms the default behavior. We don't specify every keyword; if the default is what we want, we leave it out.
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