Results Gallery

Nanofactory_1

See the Nanofactory_1 simulation page for an introduction to, and description, of this experiment.

Table of Contents

1. Experimental process
2. Results format explanation
3. Results
    a. Loaded Tooltips
         DC10c C100GeATD C100GeATS C100GeATSr5 C100GeATSr6 C100GeCTS
         C110GeS C111Ge3 AdamGe22 AdamGe33 Diad3Ge22 DCB55AGe
         DCB55BGe DCB55CGe DCB57Ge DCB5Ge DCB65Ge DCB6Ge
         DCB75Ge DCBIceane7Ge MCB55Ge MCB57Ge MCB5Ge MCB75Ge
         TwistaneGe
    b. Unloaded Tooltips
         DC10c C100GeATD C100GeATS C100GeATSr5 C100GeATSr6 C100GeCTS
         C110GeS C111Ge3 AdamGe22 AdamGe33 Diad3Ge22 DCB55AGe
         DCB55BGe DCB55CGe DCB57Ge DCB5Ge DCB65Ge DCB6Ge
         DCB75Ge DCBIceane7Ge MCB55Ge MCB57Ge MCB5Ge MCB75Ge
         TwistaneGe
    c. Q-SMAKAS Method Evaluation Molecules
         Biotin
         Heptane
         Octane

Unloaded Tooltips

DC10c

DC10c.U.pdb
Mode: Normal
Energy: -648.01479 Hartrees
DC10c.U.355q.pdb
Mode: Hydrogen Inversion
Energy: -647.88153 Hartrees		 Deforms that minimized to the alternate mode:
50 in MD run: 6000 K (~0.04 RMSD)

Notes: One or more hydrogens inverted to inside the tooltip. Ignorable - see The "Catalytic Handwaving" of Inverted Hydrogen Atoms


DC10c.U.889q.pdb
Mode: Un-classified
Energy: -648.00601 Hartrees		 Deforms that minimized to the alternate mode:
10 in MD run: 6000 K (~0.04 RMSD)

Dimer cracked.


DC10c.U.159q.pdb
Mode: Un-classified
Energy: -647.95973 Hartrees		 Deforms that minimized to the alternate mode:
9 in MD run: 6000 K (~0.04)

Notes: Carbons near the (absent) dimer compress and bond.


DC10c.U.259q.pdb
Mode: Un-classified
Energy: -648.02023 Hartrees		 Deforms that minimized to the alternate mode:
1 in MD run: 6000 K (~0.04 RMSD)

Notes: Shift in carbon arrangement to lower energy mode.

Input files:
DC10c.U.q.tar.gz [1.4 Mb]6000 K (~0.04 RMSD)1000 samples
Result files:
DC10c.U.results.q.tar.gz [18 Mb]
C100GeATD

1_C100GeATD.U.pdb
Mode: Normal
Energy: -5206.10702 Hartrees
1_C100GeATD.U.18s.pdb
Mode: Hydrogen Inversion
Energy: -5205.92499 Hartrees		 Deforms that minimized to the alternate mode:
34 in MD run: 5000 K (~0.04 RMSD)

Notes: One or more hydrogens inverted to inside the tooltip. Ignorable - see The "Catalytic Handwaving" of Inverted Hydrogen Atoms


1_C100GeATD.U.861s.pdb
Mode:
  Un-classified
Energy: -5206.04417 Hartrees		 Deforms that minimized to the alternate mode:
2 in MD run: 5000 K (~0.04 RMSD)

Notes: Dimer end of tooltip opens up.


1_C100GeATD.U.627s.pdb
Mode:
  Un-classified
Energy: -5205.94785 Hartrees		 Deforms that minimized to the alternate mode:
2 in MD run: 5000 K (~0.04 RMSD)

Notes: Dimer cracks at base.


1_C100GeATD.U.59s.pdb
Mode:
  Un-classified
Energy: -5206.12363 Hartrees		 Deforms that minimized to the alternate mode:
1 in MD run: 5000 K (~0.04 RMSD)

Notes: Hydrogen migrates to dimer carbon.

Input files:
1_C100GeATD.U.s.tar.gz [2.2 Mb]5000 K (~0.04 RMSD)1000 samples
Result files:
1_C100GeATD.U.results.s.tar.gz [12 Mb]
C100GeATS

1_C100GeATS.U.pdb
Mode: Normal?
It collapses somewhat - is it
then re-loadable?
Energy: -5206.15515 Hartrees
1_C100GeATS.U.677t.pdb
Mode: Hydrogen Inversion
Energy: -5205.94069 Hartrees		 Deforms that minimized to the alternate mode:
106 in MD run: 4500 K (~0.04 RMSD)

Notes: One or more hydrogens inverted to inside the tooltip. Ignorable - see The "Catalytic Handwaving" of Inverted Hydrogen Atoms


1_C100GeATS.U.350t.pdb
Mode: Un-classified
Energy: -5206.94812 Hartrees		 Deforms that minimized to the alternate mode:
3 in MD run: 4500 K (~0.04 RMSD)

Notes: Dimer cracks.


1_C100GeATS.U.626t.pdb
Mode: Un-classified
Energy: -5206.04239 Hartrees		 Deforms that minimized to the alternate mode:
1 in MD run: 4500 K (~0.04 RMSD)

Notes: Dimer end of tooltip opens up (version 1.)


1_C100GeATS.U.412t.pdb
Mode: Un-classified
Energy: -5206.11951 Hartrees		 Deforms that minimized to the alternate mode:
2 in MD run: 4500 K (~0.04 RMSD)

Notes: Dimer end of tooltip opens up (version 2.)

Input files:
1_C100GeATS.U.t.tar.gz [2.2 Mb]4500 K (~0.04 RMSD)1000 samples
Result files:
1_C100GeATS.U.results.t.tar.gz [33 Mb]
C100GeATSr5

1_C100GeATSr5.U.pdb
Mode: Normal
Energy: -4630.63055 Hartrees		 No alternate modes detected, but why isn't the Normal mode tooltip perfectly symmetric as one would expect?
Input files:
1_C100GeATSr5.U.w.tar.gz [1.4 Mb]3000 K (~0.04 RMSD)1000 samples
Result files:
1_C100GeATSr5.U.results.w.tar.gz [26 Mb]
C100GeATSr6
Energy minimization convergence was not achieved in the alloted time for this tooltip.
C100GeCTS

1_C100GeCTS.U.pdb
Mode: Normal?
Is it re-loadable like this?
Energy: -5208.55594 Hartrees
1_C100GeCTS.U.691w.pdb
Mode: Un-classified
Energy: -5208.37849 Hartrees		 Deforms that minimized to the alternate mode:
2 in MD run: 3000 K (~0.04 RMSD)

Notes: Looks like a better un-loaded normal mode for this tooltip, but is at a much higher energy.


1_C100GeCTS.U.970w.pdb
Mode: Un-classified
Energy: -5208.51679 Hartrees		 Deforms that minimized to the alternate mode:
1 in MD run: 3000 K (~0.04 RMSD)

Notes: Hydrogen migrated to the dimer end of tooltip.


1_C100GeCTS.U.905w.pdb
Mode: Hydrogen Inversion
Energy: -5208.34051 Hartrees		 Deforms that minimized to the alternate mode:
127 in MD run: 3000 K (~0.04 RMSD)

Notes: One or more hydrogens inverted to inside the tooltip. Ignorable - see The "Catalytic Handwaving" of Inverted Hydrogen Atoms

Input files:
1_C100GeCTS.U.w.tar.gz [2.3 Mb]3000 K (~0.04 RMSD)1000 samples
Result files:
1_C100GeCTS.U.results.w.tar.gz [69 Mb]
C110GeS

2_C110GeS.U.pdb
Mode: Normal
Energy: -4411.01682 Hartrees
2_C110GeS.U.304v.pdb
Mode: Un-classified
Energy: -4411.00630 Hartrees		 Deforms that minimized to the alternate mode:
54 in MD run: 3500 K (~0.04 RMSD)

Notes: Hydrogen from one of the Ges migrated to the other Ge


2_C110GeS.U.635v.pdb
Mode: Un-classified
Energy: -4410.94425 Hartrees		 Deforms that minimized to the alternate mode:
1 in MD run: 3500 K (~0.04 RMSD)

Notes: Dimer end of tooltip opens up.


2_C110GeS.U.671v.pdb
Mode: Hydrogen Inversion
Energy: -4410.83639 Hartrees		 Deforms that minimized to the alternate mode:
16 in MD run: 3500 K (~0.04 RMSD)

Notes: One or more hydrogens inverted to inside the tooltip. Ignorable - see The "Catalytic Handwaving" of Inverted Hydrogen Atoms

Input files:
2_C110GeS.U.v.tar.gz [1.2 Mb]3500 K (~0.04 RMSD)1000 samples
Result files:
2_C110GeS.U.results.v.tar.gz [11 Mb]
C111Ge3
Energy minimization convergence was not achieved in the alloted time for this tooltip.
AdamGe22

5_AdamGe22.U.pdb
Mode: Normal
Energy: -4372.42441 Hartrees
5_AdamGe22.U.742w.pdb
Mode: Un-classified
Energy: -4372.40720 Hartrees		 Deforms that minimized to the alternate mode:
94 in MD run: 3000 K (0.0402 RMSD)

Notes: Hydrogen from one of the Ges migrated to the other Ge.


5_AdamGe22.U.724w.pdb
Mode: Un-classified
Energy: -4372.31910 Hartrees		 Deforms that minimized to the alternate mode:
1 in MD run: 3000 K (0.0402 RMSD)

Notes: Dimer end of tooltip opens up.

Input files:
5_AdamGe22.U.w.tar.gz [1.1 Mb]3000 K (0.0402 RMSD)1000 samples
Result files:
5_AdamGe22.U.results.w.tar.gz [10 Mb]
AdamGe33

5_AdamGe33.U.pdb
Mode: "Normal"
Energy: -4373.66814 Hartrees
5_AdamGe33.U.597z.pdb
Mode: Un-classified
Energy: -4373.66585 Hartrees		 Deforms that minimized to the alternate mode:
2 in MD run: 1500 K (0.04345 RMSD)

Notes: Carbon migrates to dimer position.


5_AdamGe33.U.350z.pdb
Mode: Un-classified
Energy: -4373.57746 Hartrees		 Deforms that minimized to the alternate mode:
50 in MD run: 1500 K (0.04345 RMSD)

Notes: Hydrogen from one of the Ges migrated to the other Ge.


5_AdamGe33.U.216z.pdb
Mode: Un-classified
Energy: -4373.56241 Hartrees		 Deforms that minimized to the alternate mode:
299 in MD run: 1500 K (0.04345 RMSD)

Notes: Dimer end of tooltip opens up.

Input files:
5_AdamGe33.U.z.tar.gz [1.3 Mb]1500 K (0.04345 RMSD)1000 samples
Result files:
5_AdamGe33.U.results.z.tar.gz [24 Mb]
Diad3Ge22

6_Diad3Ge22.U.pdb
Mode: Normal
Energy: -4708.26935 Hartrees
6_Diad3Ge22.U.951w.pdb
Mode: Un-classified
Energy: -4708.35254 Hartrees		 Deforms that minimized to the alternate mode:
58 in MD run: 3000 K (~0.04 RMSD)

Notes: Hydrogen from one of the Ges migrated to the other Ge. Lower energy configuration.


6_Diad3Ge22.U.20w.pdb
Mode: Un-classified
Energy: -4708.26935 Hartrees		 Deforms that minimized to the alternate mode:
?? in MD run: 3000 K (0.04 RMSD)

Notes: Ge hydrogens changed sides. Detected via visual inspection of the MD run - otherwise it has the same energy as the normal mode tooltip. Counting them would be a pain because we'd have to do it manually/visually since energy gives no indication. Come up with an algorithm to automatically detect symmetric deformations by labeling a select triple/triangle of atoms, then do a fuzzy comparison to atoms in the immediate vicinity of the binding pocket.


6_Diad3Ge22.U.872w.pdb
Mode: Un-classified
Energy: -4708.24500 Hartrees		 Deforms that minimized to the alternate mode:
82 in MD run: 3000 K (0.04 RMSD)

Notes: One Ge hydrogen switched sides.


6_Diad3Ge22.U.312w.pdb
Mode: Hydrogen Inversion
Energy: -4708.10811 Hartrees		 Deforms that minimized to the alternate mode:
1 in MD run: 3000 K (0.04 RMSD)

Notes: One or more hydrogens inverted to inside the tooltip. Ignorable - see The "Catalytic Handwaving" of Inverted Hydrogen Atoms

Input files:
6_Diad3Ge22.U.w.tar.gz [1.5 Mb]3000 K (~0.04 RMSD)1000 samples
Result files:
6_Diad3Ge22.U.results.w.tar.gz [28 Mb]
DCB55AGe

7_DCB55AGe.U.pdb
Mode: Normal
Energy: -4668.29204 Hartrees
7_DCB55AGe.U.607u.pdb
Mode: Hydrogen Inversion
Energy: -4668.21919 Hartrees		 Deforms that minimized to the alternate mode:
86 in MD run: 4000 K (~0.04 RMSD)

Notes: One or more hydrogens inverted to inside the tooltip. Ignorable - see The "Catalytic Handwaving" of Inverted Hydrogen Atoms


7_DCB55AGe.U.3u.pdb
Mode: Un-classified
Energy: -4668.28585 Hartrees		 Deforms that minimized to the alternate mode:
12 in MD run: 4000 K (0.04 RMSD)

Notes: Dimer end of tooltip opens up.


7_DCB55AGe.U.630u.pdb
Mode: Un-classified
Energy: -4668.33716 Hartrees		 Deforms that minimized to the alternate mode:
18 in MD run: 4000 K (0.04 RMSD)

Notes: Dimer end of tooltip opens up. Lower energy configuration.

Input files:
7_DCB55AGe.U.u.tar.gz [1.5 Mb]4000 K (~0.04 RMSD)1000 samples
Result files:
7_DCB55AGe.U.results.u.tar.gz [26 Mb]
DCB55BGe

7_DCB55BGe.U.pdb
Mode: Normal
Energy: -4714.86335 Hartrees
7_DCB55BGe.U.681z.pdb
Mode: Un-classified
Energy: -4714.89054 Hartrees		 Deforms that minimized to the alternate mode:
1 in MD run: 1500 K (0.05275 RMSD)

Notes: Base opens up into lower energy configuration Ð version 1.


7_DCB55BGe.U.928z.pdb
Mode: Un-classified
Energy: -4714.86385 Hartrees		 Deforms that minimized to the alternate mode:
278 in MD run: 1500 K (0.05275 RMSD)

Notes: Base opens up into lower energy configuration Ð version 2.


7_DCB55BGe.U.978z.pdb
Mode: Un-classified
Energy: -4714.85551 Hartrees		 Deforms that minimized to the alternate mode:
116 in MD run: 1500 K (0.05275 RMSD)

Notes: A Ge is in an odd position.

Input files:
7_DCB55BGe.U.z.tar.gz [1.6 Mb]1500 K (0.05275 RMSD)1000 samples
Result files:
7_DCB55BGe.U.results.z.tar.gz [43 Mb]
DCB55CGe

7_DCB55CGe.U.pdb
Mode: Normal
Energy: -4752.28751 Hartrees
7_DCB55CGe.U.160u.pdb
Mode: Hydrogen Inversion
Energy: -4752.23201 Hartrees		 Deforms that minimized to the alternate mode:
214 in MD run: 4000 K (0.04297 RMSD)

Notes: One or more hydrogens inverted to inside the tooltip. Ignorable - see The "Catalytic Handwaving" of Inverted Hydrogen Atoms


7_DCB55CGe.U.81u.pdb
Mode: Un-classified
Energy: -4752.23922 Hartrees		 Deforms that minimized to the alternate mode:
1 in MD run: 4000 K (0.04297 RMSD)

Notes: A hydrogen migrates to a Ge.


7_DCB55CGe.U.701u.pdb
Mode: Un-classified
Energy: -4752.26221 Hartrees		 Deforms that minimized to the alternate mode:
1 in MD run: 4000 K (0.04297 RMSD)

Notes: Dimer end of tooltip opens up.

Input files:
7_DCB55CGe.U.u.tar.gz [1.6 Mb]4000 K (0.04297 RMSD)1000 samples
Result files:
7_DCB55CGe.U.results.u.tar.gz [29 Mb]
DCB57Ge

7_DCB57Ge.U.pdb
Mode: Normal
Energy: -4783.61893 Hartrees
7_DCB57Ge.U.308u.pdb
Mode: Hydrogen Inversion
Energy: -4783.53637 Hartrees		 Deforms that minimized to the alternate mode:
131 in MD run: 4000 K (~0.04 RMSD)

Notes: One or more hydrogens inverted to inside the tooltip. Ignorable - see The "Catalytic Handwaving" of Inverted Hydrogen Atoms


7_DCB57Ge.U.969u.pdb
Mode: Un-classified
Energy: -4783.59790 Hartrees		 Deforms that minimized to the alternate mode:
2 in MD run: 4000 K (~0.04 RMSD)

Notes: Dimer end of tooltip opens up.


7_DCB57Ge.U.998u.pdb
Mode: Un-classified
Energy: -4783.62681 Hartrees		 Deforms that minimized to the alternate mode:
1 in MD run: 4000 K (~0.04 RMSD)

Notes: Dimer end of tooltip opens up. Lower energy configuration..

Input files:
7_DCB57Ge.U.u.tar.gz [1.6 Mb]4000 K (~0.04 RMSD)1000 samples
Result files:
7_DCB57Ge.U.results.u.tar.gz [22 Mb]
DCB5Ge

7_DCB5Ge.U.pdb
Mode: Normal
Energy: -4745.90633 Hartrees
7_DCB5Ge.U.237x.pdb
Mode: Hydrogen Inversion
Energy: -4745.89682 Hartrees		 Deforms that minimized to the alternate mode:
132 in MD run: 2500 K (~0.04 RMSD)

Notes: One or more hydrogens inverted to inside the tooltip. Ignorable - see The "Catalytic Handwaving" of Inverted Hydrogen Atoms


7_DCB5Ge.U.950x.pdb
Mode: Un-classified
Energy: -4745.92874 Hartrees		 Deforms that minimized to the alternate mode:
3 in MD run: 2500 K (~0.04 RMSD)

Notes: Dimer end of tooltip opens up. Lower energy configuration..

Input files:
7_DCB5Ge.U.x.tar.gz [1.6 Mb]2500 K (~0.04 RMSD)1000 samples
Result files:
7_DCB5Ge.U.results.x.tar.gz [32 Mb]
DCB65Ge

7_DCB65Ge.U.pdb
Mode: Normal
Energy: -4861.24561 Hartrees
7_DCB65Ge.U.155v.pdb
Mode: Hydrogen Inversion
Energy: -4861.21590 Hartrees		 Deforms that minimized to the alternate mode:
100 in MD run: 3500 K (~0.04 RMSD)

Notes: One or more hydrogens inverted to inside the tooltip. Ignorable - see The "Catalytic Handwaving" of Inverted Hydrogen Atoms

Input files:
7_DCB65Ge.U.v.tar.gz [1.8 Mb]3500 K (~0.04 RMSD)1000 samples
Result files:
7_DCB65Ge.U.results.v.tar.gz [22 Mb]
DCB6Ge
Energy minimization convergence was not achieved in the alloted time for this tooltip.
DCB75Ge

7_DCB75Ge.U.pdb
Mode: Normal
Energy: -5021.31216 Hartrees
7_DCB75Ge.U.381y.pdb
Mode: Hydrogen Inversion
Energy: -5021.28496 Hartrees		 Deforms that minimized to the alternate mode:
6 in MD run: 2000 K (~0.04 RMSD)

Notes: One or more hydrogens inverted to inside the tooltip. Ignorable - see The "Catalytic Handwaving" of Inverted Hydrogen Atoms

Input files:
7_DCB75Ge.U.y.tar.gz [2.2 Mb]2000 K (~0.04 RMSD)1000 samples
Result files:
7_DCB75Ge.U.results.y.tar.gz [50 Mb]
DCBIceane7Ge

7_DCBIceane7Ge.U.pdb
Mode: Normal
Energy: -4555.37220 Hartrees
7_DCBIceane7Ge.U.10w.pdb
Mode: Un-classified
Energy: -4555.36938 Hartrees		 Deforms that minimized to the alternate mode:
115 in MD run: 3000 K (~0.04 RMSD)

Notes: Hydrogen from one of the Ges migrated to the other Ge.


7_DCBIceane7Ge.U.431w.pdb
Mode: Un-classified
Energy: -4555.35033 Hartrees		 Deforms that minimized to the alternate mode:
3 in MD run: 3000 K (~0.04 RMSD)

Notes: Dimer cracks.

Input files:
7_DCBIceane7Ge.U.w.tar.gz [1.4 Mb]3500 K (~0.04 RMSD)1000 samples
Result files:
7_DCBIceane7Ge.U.results.w.tar.gz [20 Mb]
MCB55Ge

7_MCB55Ge.U.pdb
Mode: Normal
Energy: -4753.34967 Hartrees		 No alternate modes detected.
Input files:
7_MCB55Ge.U.z.tar.gz [1.7 Mb]1500 K (0.04399 RMSD)1000 samples
Result files:
7_MCB55Ge.U.results.z.tar.gz [47 Mb]
MCB57Ge
Energy minimization convergence was not achieved in the alloted time for this tooltip.
MCB5Ge

7_MCB5Ge.U.pdb
Mode: Normal
Energy: -4868.10357 Hartrees		 No alternate modes detected.
Input files:
7_MCB5Ge.U.z.tar.gz [1.9 Mb]2000 K (~0.04 RMSD)1000 samples
Result files:
7_MCB5Ge.U.results.z.tar.gz [55 Mb]
MCB75Ge
Energy minimization convergence was not achieved in the alloted time for this tooltip.
TwistaneGe
Energy minimization convergence was not achieved in the alloted time for this tooltip.