Hello Vitaly--
>
> I've noticed that the manual page for the "eefxPotTools" now makes
> reference to the lipid bilayer thickness. Does this mean that
> XPLOR-NIH now includes the implicit membrane model? If this has
> already been implemented in the public release, could you please share
> a sample script for using this potential?
>
Good catch. The paper isn't quite yet accepted, and I don't have the
example scripts prepared, but here's a snippet which should work with
Xplor-NIH 2.39.
best regards--
Charles
from eefxPotTools import create_EEFxPot, param_LK, setCenter
eefx=create_EEFxPot("eefx","ALL",paramSet=param_LK)
eefx.setScale(1)
#eefx.setVerbose(1)
eefx.setIMM1(True)
eefx.useGROUp(1)
eefx.setMoveTol(0.5)
print eefx.showParam()
eefx.setThickness(20) # IMM membrane thickness
eefx.setProfileN(10) # IMM n parameter of membrane profile
eefx.setA(0.85) # IMM a value that scales dielectric screening.
pots.append(eefx)
highTempParams.append(StaticRamp("eefx.setScale(0.004)"))
rampedParams.append(MultRamp(0.004,1.0,"eefx.setScale(VALUE)"))
IMM_com = "resid 1:148 and (name CA)" # Center of mass selection for IMMx
center (z=0).
setCenter(IMM_com) # translate selected center of mass to
IMMx z=0.
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