330.0350330350.085filenamepage5$1.mmldate1228322282000url/Users/freichsman/Documents/Projects/Concord/activities/proteins-III/proteins-III-live/page5$1.mmlsize123104codebase/Users/freichsman/Documents/Projects/Concord/activities/proteins-III/proteins-III-livecontrol the temperature of the two types of particles.20Two-part heat bathshow selectionhalo off;
select element 0;
set kelvin 2000;
select element 1;
set kelvin 300;
select element none;
show selectionhalo on;
if(%model_time < 100);
select element 2;
set kelvin 1000*rand();
select element 1;
set kelvin 1000*rand();
select element none;
endif;
Search one ligand that enters the binding pocket and cause it to bind.20Binderset %i nearesttoatom(2, 2, 3);
if(%i!=-1);
set atom[%i].charge -0.2;
endif;Removerset %i nearesttoatom(25, 2, 3);
if(%i!=-1);
set atom[%i].charge +0.5;
endif;3.0None140.02class org.concord.mw2d.models.Atom210140.0-14.090.0membraneBkgStretched2.gif2550255255membraneOnly.gif216.58401296406959351.9452155493767123pgk-charged-2.gif-0.0438400522-5.040.0pgk-ligand-charged2.gif-1.69298024class org.concord.mw2d.models.RadialBond13-1.134464279.077.0pgk-ligand-charged2.gif-1.633387312class org.concord.mw2d.models.RadialBond14-1.134464225.62996900709084259.9010404146034pgk-ligand-charged2.gif-0.7180698520class org.concord.mw2d.models.RadialBond25-1.134464168.95908745187972196.32872501100132pgk-ligand-charged2.gif3.070111828class org.concord.mw2d.models.RadialBond16-1.134464289.0190.0ligand-wrong-charge.gif-0.0593882841class org.concord.mw2d.models.RadialBond17-1.134464142.0120.0ligand-wrong-charge.gif-0.3945420749class org.concord.mw2d.models.RadialBond18-1.13446489.0247.0ligand-wrong-charge.gif-2.3115357class org.concord.mw2d.models.RadialBond19-1.134464207.090.0ligand-wrong-shape.gif0.04741965236class org.concord.mw2d.models.RadialBond1101.5707964224.0149.0ligand-wrong-shape.gif2.208272265class org.concord.mw2d.models.RadialBond1111.5707964229.022.0ligand-wrong-shape.gif1.588679470class 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