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As a rule of thumb we expect that the energy coming from the local interactions should be around 1/3 of the the same as the non-local interactions. We can use the expectations to approximate the energy change in the Unfolding of CRISPR. Following this rule a SMF of 0.05 should be ok.
| Energy | Energy change | Energy change | between Q=1 and Q=0 | ||||||||
| SMF=0.01 | SMF=0.02 | SMF=0.0105 | SMF=0.2 | Change_expected | SMF=0.01 | SMF=0.02 | SMF=0.05 | SMF=0.2 | |||
| ${Step} | 1000 | 1000 | 1000 | 1000 | |||||||
| ${E_chain} | 1103.63 | 1146.4059105198 | 1132.9169298699 | 1066.13 | 142.39% | 1571.49 | 1632.40 | 1613.20 | 1518.09 | ||
| ${E_bond} | 3719.19 | 4496.0767517408 | 4666.2099846672 | 3591.47 | -66.16% | -2460.76 | -2974.78 | -3087.35 | -2376.26 | ||
| ${E_chi} | 311.13 | 332.9247833235 | 328.6440389852 | 270.81 | 194.72% | 605.81 | 648.26 | 639.92 | 527.30 | ||
| ${E_rama} | -5324.09 | -5358.8095694418 | -5346.4451338263 | -5215.35 | 5.44% | -289.41 | -291.30 | -290.63 | -283.50 | ||
| ${E_excl} | 70.33 | 71.7741816843 | 75.6873593073 | 111.11 | -145.26% | -102.16 | -104.26 | -109.95 | -161.40 | ||
| ${E_dssp} | -76.22 | -86.6894737573 | -90.0003437801 | -102.85 | -67.69% | 51.59 | 58.68 | 60.92 | 69.62 | ||
| ${E_pap} | -78.58 | -79.8398802165 | -87.8172993273 | -93.15 | 83.73% | -65.79 | -66.85 | -73.53 | -78.00 | ||
| ${E_water} | -752.31 | -774.4315400479 | -736.5138566067 | -524.77 | 89.06% | -670.04 | -689.74 | -655.97 | -467.38 | ||
| ${E_helix} | -229.17 | -223.4311335965 | -241.1245561557 | -283.44 | -23.52% | 53.90 | 52.55 | 56.71 | 66.67 | ||
| ${E_fmem} | -54.26 | -111.0323591108 | -344.3669434681 | -5632.65 | 100.00% | -54.26 | -111.03 | -344.37 | -5632.65 | ||
| ${E_P} | -1310.35 | -587.0523289023 | -642.8098203344 | -6812.70 | -105.00% | 1375.92 | 616.43 | 674.98 | 7153.62 | ||
| Local | -5607.52 | -5693.27 | -5931.94 | -11131.44 | -289.77 | -349.78 | -578.28 | -5849.49 | |||
| NonLocal | -907.11 | -906.11 | -905.11 | -720.78 | -684.24 | -697.91 | -668.58 | -475.77 | |||
| Others | 5204.27 | 5205.27 | 5206.27 | 5039.52 | -385.62 | -798.38 | -944.17 | -492.27Local | |||
| +Non-local | Local+Non-local | -974.0133132415 | -1047.6945030493 | -1246.863190185 | -6325.2556957897 | ||||||
| Local% | Local% | 29.75% | 33.39% | 46.38% | 92.48% | ||||||
| NonLocal% | NonLocal% | 70.25% | 66.61% | 53.62% | 7.52% | ||||||
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Crispr-Cas9 + DNA
Due to a mistake I didn't update the neighbor list, so it is possible to see an overlap between two domains (grey and red). The single memory force was turned off in this simulation.
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