错误“Out of range atoms - cannot compute PPPM (../pppm.cpp:1937)”的典型报告为：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)
这一步显示后，就exit了。目前来说，彷佛惟一可行的方案就是调整原子的初始构型（不合理的初始构型会致使局部的受力太大），时间步调小或者 negibor list 增大基本不凑效。这种调整构型手工很难办成，即便是利用最小化的方案，通常也不宜用同一种力场来进行调整。下面这个调整就是在ChemBio3D 下利用MM2最小化完成的，效果还不错：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
该步骤不只指出了缘由，也给出了迭代步骤，最后还计算了各类能量的大小。在完成这个初步调整的基础上，咱们比较了一下两种结构的差异：ide
其中黄色是调整前的不理想的初始结构，绿色是在此基础上利用MM2力场调整的结构。经过这个步骤输出的pdb文件就能够在lammps里面顺利运行了：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
经过这个初始结构的运行结构对比，还能够进一步启发对于蛋白质链自相互做用机理的研究，这里暂不赘述。atom
参考连接：spa
[1] lammps运行一段时间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