ORCA笔记：Histidine
原子坐标
原子坐标通常可以通过用Avogadro打开相应原子的cif文件读取。cif文件可以从Crystallography Open Database得到。首页左侧有Search，输入必要的物质名称、化学式、元素等信息即可获得结果。
另一种方式是在Avogadro中，File->Import->Fetch by chemical name，输入英文名称，一般能获得分子结构。
获得分子结构文件后，即可将原子坐标置入ORCA的输入文件。
ORCA输入文件
# avogadro generated ORCA input file # Basic Mode # Histidine ! RKS # Restricted Kohn-Sham Method ! IGLO-II # NMR recomended basis set ! TightSCF # SCF threshold criteria ! Opt # Geometry Optimization Run %method Grid 4 # Lebedev 320 points (NMR recomended) end %output Print [ P_Hirshfeld ] 1 # Hirshfeld Charge Population Print [ P_Mayer ] 1 # Mayer Bond Orders end * xyz 0 1 O 3.0421000000 -1.3483000000 -0.1369000000 O 3.1858000000 0.8565000000 -0.1766000000 N -1.8374000000 -0.9336000000 0.5491000000 N -3.3926000000 0.3473000000 -0.2238000000 N 0.8440000000 1.3644000000 0.9686000000 C 2.5082000000 -0.1258000000 0.0123000000 C -3.1036000000 -0.6362000000 0.6553000000 C -2.2334000000 0.6536000000 -0.8842000000 C -1.2766000000 -0.1527000000 -0.3862000000 C 0.1694000000 -0.1778000000 -0.8101000000 C 1.0636000000 0.0214000000 0.4153000000 H 3.9726000000 -1.3923000000 -0.3965000000 H -3.8051000000 -1.1023000000 1.3314000000 H -4.2597000000 0.7597000000 -0.3616000000 H -2.1097000000 1.3989000000 -1.6559000000 H 0.3958000000 -1.1384000000 -1.2728000000 H 0.3518000000 0.6228000000 -1.5270000000 H -0.1015000000 1.4665000000 1.3056000000 H 1.0642000000 2.0762000000 0.2882000000 H 0.8187000000 -0.7266000000 1.1693000000 * %eprnmr Ori OwnNuc # alternative OwnNuc IGLO LocMet FB # localization method for IGLO # FB=Foster-Boys PM=PipekMezey (default) Nuclei = all { shift } end
“基础版”输入文件如上。!开头的行是ORCA的Keyword，%和end 中间的内容是一些选项。再下面是原子坐标。#标志注释。Keyword不区分大小写。
!tightSCF指定了SCF收敛标准的宽松与严格，所有选项如下：NORMALSCF LOOSESCF SLOPPYSCF STRONGSCF TIGHTSCF VERYTIGHTSCF EXTREMESCF
!IGLO-II指定了NMR和EPR计算的基础集，IGLO-III是IGLO-II的扩展版，据称计算精度更高。实际使用发现IGLO-III的计算耗时远大于IGLO-II。
计算中进行结构优化收敛，每循环一次会检查一次收敛结果，如果未收敛则继续循环，直至满足收敛标准。
.--------------------.
----------------------|Geometry convergence|-------------------------
Item value Tolerance Converged
---------------------------------------------------------------------
Energy change -0.0000064351 0.0000050000 NO
RMS gradient 0.0000753876 0.0001000000 YES
MAX gradient 0.0003317471 0.0003000000 NO
RMS step 0.0025081186 0.0020000000 NO
MAX step 0.0087154659 0.0040000000 NO
........................................................
Max(Bonds) 0.0004 Max(Angles) 0.06
Max(Dihed) 0.50 Max(Improp) 0.00
---------------------------------------------------------------------
The optimization has not yet converged - more geometry cycles are needed
收敛标准可以通过设置收敛检查模式来调整。ORCA手册中提到tightSCF对应的设定为：
%scf TolE 1e-8 # energy change between two cycles TolRMSP 5e-9 # RMS density change TolMaxP 1e-7 # maximum density change TolErr 5e-7 # DIIS error convergence TolG 1e-5 # orbital gradient convergence TolX 1e-5 # orbital rotation angle convergence ConvCheckMode 2 # = 0: check all convergence criteria # = 1: stop if one of criterion is met, this is sloppy! # = 2: check change in total energy and in one-electron energy # Converged if delta(Etot)<TolE and delta(E1)<1e3*TolE ConvForced # = 0: convergence not mandatory for next calculation step # = 1: break, if you did not meet the convergence criteria end
ConvCheckMode为0时，必须满足所有收敛条件；为1时，只需满足一个收敛条件（很宽松）；为2时，说明如文档中所述。默认为2。
在计算复杂分子（例如Histidine）时，采用Mode 2会计算到仅有Max step不满足条件的情况：
.--------------------. ----------------------|Geometry convergence|------------------------- Item value Tolerance Converged --------------------------------------------------------------------- Energy change -0.0000030086 0.0000050000 YES RMS gradient 0.0000563025 0.0001000000 YES MAX gradient 0.0002610986 0.0003000000 YES RMS step 0.0017001510 0.0020000000 YES MAX step 0.0054510309 0.0040000000 NO ........................................................ Max(Bonds) 0.0004 Max(Angles) 0.07 Max(Dihed) 0.31 Max(Improp) 0.00 --------------------------------------------------------------------- The energies and gradients are converged and the convergence on bond distances, angles, dihedrals and impropers is acceptable. Convergence will therefore be signaled now
如果使用Mode 0，在输入文件中加入如下内容：
%scf ConvCheckMode 0 # = 0: check all convergence criteria # = 1: stop if one of criterion is met, this is sloppy! # = 2: check change in total energy and in one-electron energy # Converged if delta(Etot)<TolE and delta(E1)<1e3*TolE end
最终Max step仍然是no：
.--------------------. ----------------------|Geometry convergence|------------------------- Item value Tolerance Converged --------------------------------------------------------------------- Energy change -0.0000007943 0.0000050000 YES RMS gradient 0.0000490074 0.0001000000 YES MAX gradient 0.0002748563 0.0003000000 YES RMS step 0.0016925958 0.0020000000 YES MAX step 0.0046326004 0.0040000000 NO ........................................................ Max(Bonds) 0.0003 Max(Angles) 0.06 Max(Dihed) 0.27 Max(Improp) 0.00 --------------------------------------------------------------------- The energies and gradients are converged and the convergence on bond distances, angles, dihedrals and impropers is acceptable. Convergence will therefore be signaled now
不知是否是输入文件语法错误？（后记：前面添加的CheckMode适用于SCF收敛，而非结构优化收敛，因此不会做用到结构优化上）
计算耗时
在使用IGLO-III和ConvCheckMode 0的情况下，在云端计算了21小时10分钟；使用IGLO-III和Mode 2，在本地计算耗时5小时23分钟；使用IGLO-II和Mode 2在云端计算耗时1小时26分钟。