i used CHARMM-GUI membrane builder module to prepare the necessary files for simulating a membrane using NAMD and while inspecting the configuration input files, i noticed that it uses collective variables (ColVar) to apply a harmonic potential on some atoms of the head groups of the lipids during equilibration only. why would i need to apply these potentials? and why selecting the centers values to be of these specific values (ex: 18 for the cholesterol lipid)?
these are the first and last colvar lines included in the first equilibration step:
###Lipid Head###
Colvarstrajfrequency 100
Colvarsrestartfrequency 100
colvar {
name chl1_head_upper
distanceZ {
ref {
dummyAtom ( 0.000, 0.000, 0.000 )
}
main {
atomsFile restraints/chl1_head_upper.ref
atomsCol B
atomsColValue 1.0
}
}
}
harmonic {
colvars chl1_head_upper
centers 18
forceConstant 5
}
....
....
....
colvar {
name psm_head_lower
distanceZ {
ref {
dummyAtom ( 0.000, 0.000, 0.000 )
}
main {
atomsFile restraints/psm_head_lower.ref
atomsCol B
atomsColValue 1.0
}
}
}
harmonic {
colvars psm_head_lower
centers -21
forceConstant 5
}
I think it is important to make some restraints on the membrane to not lose the bilayer configuration when preparing the system for the simulation.
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