Dear Charles,
Thank you, it's working well! Just to clarify, is this potential meant
to replace 'VDW' (as in your JMR 2014 paper), or to be used in
conjunction with it?
Vitaly
On Wed, Jun 17, 2015 at 12:59 PM, Charles Schwieters
<char...@schwieters.org> wrote:
>
> 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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