錯誤「Out of range atoms - cannot compute PPPM (../pppm.cpp:1937)」的典型報告爲：html
---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -nan KinEng = 0.0000 Temp = 0.0000 PotEng = -nan E_bond = 5536.5700 E_angle = -nan E_dihed = 405.0252 E_impro = 799.1751 E_vdwl = -nan E_coul = -nan E_long = -2301.2059 Press = -nan ERROR on proc 8: Out of range atoms - cannot compute PPPM (../pppm.cpp:1937) ERROR on proc 15: Out of range atoms - cannot compute PPPM (../pppm.cpp:1937)
這一步顯示後，就exit了。目前來說，彷佛惟一可行的方案就是調整原子的初始構型（不合理的初始構型會致使局部的受力太大），時間步調小或者 negibor list 增大基本不湊效。這種調整構型手工很難辦成，即便是利用最小化的方案，通常也不宜用同一種力場來進行調整。下面這個調整就是在ChemBio3D 下利用MM2最小化完成的，效果還不錯：less
There is no secondary-structure information recorded. Bond length is unusually long: 4.79754 223-222 Bond length is unusually long: 2.70009 328-327 Bond length to Hydrogen is unusually long: 2.13469 456-457 Bond length to Hydrogen is unusually long: 2.13561 456-458 Since there is no secondary-structure information, ChemBio3D Ultra is going to formcompute it. The number of atoms in this molecule exceeds the atom synchronization limit. The ChemDraw panel cannot load the molecular structure. MM2 Calculation completed successfully ------------MM2 Minimization------------ Warning: The number of ligands attached does not match the geometry of N(1) Warning: The number of ligands attached does not match the geometry of O(139) Warning: The number of ligands attached does not match the geometry of O(453) Warning: The number of ligands attached does not match the geometry of C(457) Warning: The number of ligands attached does not match the geometry of H(458) Warning: The number of ligands attached does not match the geometry of H(459) Warning: The number of ligands attached does not match the geometry of C(559) Separating coincident atoms: C(63)-H(64) Separating coincident atoms: C(238)-H(239) Pi System: 538 536 534 533 541 543 Warning: Some parameters are guessed (Quality = 1). Iteration 1 Steric Energy 274941803.943 RMS Gradient 1341504.134 RMS Move 0.0000 Iteration 2 Steric Energy 104634145.547 RMS Gradient 628201.522 RMS Move 0.0892 Iteration 3 Steric Energy 98644711.696 RMS Gradient 619854.158 RMS Move 0.0223 Iteration 4 Steric Energy 36519658.997 RMS Gradient 278060.506 RMS Move 0.0717 Iteration 5 Steric Energy 33726135.351 RMS Gradient 272796.212 RMS Move 0.0223 Iteration 6 Steric Energy 14471590.989 RMS Gradient 125631.455 RMS Move 0.0497 Iteration 7 Steric Energy 13180439.253 RMS Gradient 125367.907 RMS Move 0.0223 ------------------------------------------------------------------ Iteration 6205 Steric Energy -157.182 RMS Gradient 0.015 RMS Move 0.0000 Iteration 6206 Steric Energy -157.182 RMS Gradient 0.011 RMS Move 0.0000 Iteration 6207 Steric Energy -157.182 RMS Gradient 0.009 RMS Move 0.0000 Iteration 6207: Minimization terminated normally because the gradient norm is less than the minimum gradient norm Stretch: 25.2323 Bend: 288.0828 Stretch-Bend: -1.1579 Torsion: 141.6311 Non-1,4 VDW: -380.2947 1,4 VDW: 148.6268 Dipole/Dipole: -379.3025 Total Energy: -157.1821 kcal/mol Calculation ended
該步驟不只指出了緣由，也給出了迭代步驟，最後還計算了各類能量的大小。在完成這個初步調整的基礎上，咱們比較了一下兩種結構的差異：ide
其中黃色是調整前的不理想的初始結構，綠色是在此基礎上利用MM2力場調整的結構。經過這個步驟輸出的pdb文件就能夠在lammps裏面順利運行了：this
---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = 6842.2689 KinEng = 0.0000 Temp = 0.0000 PotEng = 6842.2689 E_bond = 5217.8375 E_angle = 889.2725 E_dihed = 220.4900 E_impro = 1.9840 E_vdwl = 373.2779 E_coul = 2417.1047 E_long = -2277.6976 Press = -10629.6498 ---------------- Step 10 ----- CPU = 0.0337 (sec) ---------------- TotEng = 2472.8837 KinEng = 0.0000 Temp = 0.0000 PotEng = 2472.8837 E_bond = 1476.8188 E_angle = 611.9309 E_dihed = 226.6634 E_impro = 2.8918 E_vdwl = 31.9095 E_coul = 2405.3611 E_long = -2282.6917 Press = -3317.6592 ---------------- Step 20 ----- CPU = 0.0562 (sec) ---------------- TotEng = 998.0748 KinEng = 0.0000 Temp = 0.0000 PotEng = 998.0748 E_bond = 200.8747 E_angle = 453.3712 E_dihed = 234.2443 E_impro = 6.1779 E_vdwl = -6.6921 E_coul = 2397.4972 E_long = -2287.3984 Press = 1691.6034
經過這個初始結構的運行結構對比，還能夠進一步啓發對於蛋白質鏈自相互做用機理的研究，這裏暫不贅述。atom
參考連接：spa
[1] lammps運行一段時間ERROR on proc 0: Out of range atoms - cannot compute PPPM.net
[2] Re: [lammps-users] Error on proc 0: Out of range atoms - cannot compute PPPMcode