@ home ▁graph ical ▁user ▁interface ▁( G UI ) ▁is ▁a ▁screens aver ▁which ▁shows ▁a ▁current ▁work unit ' s ▁progress ▁during ▁the ▁sim ulated ▁protein ▁fol ding ▁process . ▁ ▁In ▁the ▁upper - left ▁of ▁the ▁current ▁screens aver , ▁the ▁target ▁protein ▁is ▁shown ▁adopt ing ▁different ▁shapes ▁( con form ations ) ▁in ▁its ▁search ▁for ▁the ▁lowest ▁energy ▁structure . ▁ ▁Dep icted ▁immediately ▁to ▁the ▁right ▁is ▁the ▁structure ▁of ▁the ▁most ▁recently ▁accepted . ▁ ▁On ▁the ▁upper ▁right ▁the ▁lowest ▁energy ▁con formation ▁of ▁the ▁current ▁de co y ▁is ▁shown ; ▁below ▁that ▁is ▁the ▁true , ▁or ▁native , ▁structure ▁of ▁the ▁protein ▁if ▁it ▁has ▁already ▁been ▁determined . ▁ ▁Three ▁graphs ▁are ▁included ▁in ▁the ▁screens aver . ▁ ▁Near ▁the ▁middle , ▁a ▁graph ▁for ▁the ▁accepted ▁model ' s ▁therm od ynamic ▁free ▁energy ▁is ▁displayed , ▁which ▁fl uct u ates ▁as ▁the ▁accepted ▁model ▁changes . ▁ ▁A ▁graph ▁of ▁the ▁accepted ▁model ' s ▁root - mean - square ▁deviation ▁( R MS D ), ▁which ▁measures ▁how ▁struct ur ally ▁similar ▁the ▁accepted ▁model ▁is ▁to ▁the ▁native ▁model , ▁is ▁shown ▁far ▁right . ▁ ▁On ▁the ▁right ▁of ▁the ▁accepted ▁energy ▁graph ▁and ▁below ▁the ▁R MS D ▁graph , ▁the ▁results ▁from ▁these ▁two ▁functions ▁are ▁used ▁to ▁produce ▁an ▁energy ▁vs . ▁R MS D ▁plot ▁as ▁the ▁model ▁is ▁progress ively ▁ref ined . ▁ ▁Like ▁all ▁B