目录

如何只计算部分原子的频率、相关的Gibbs自由能

注意:本说明仅适用于AMS2020及其以后的版本,之前的版本请参考:如何只计算体系部分原子的频率

注意!

频率的计算,是通过计算该构型下,能量对每个原子的二阶导数得到。很多人想象中,希望固定一些原子,使其不动,只计算一部分原子的振动,这只是一种错误、肤浅的感性的认知。

振动谱的计算,实际上并不计算运动状态,而是计算静止状态的力常数,因此根本谈不上什么“固定某些原子”,所有原子都是固定的!关心哪些原子的振动情况,就只计算这些原子的力常数(即,能量二阶梯度)。

如果不理解为什么如此,应学习相关弹性力学知识。

另外:

参数设置

首先对要冻结的部分创建为一个分区,默认名为Region_1(参考如何创建分区):

一般性参数设置,勾选Frequencies

进入Frequencies的详细设置窗口,设置MBH。务必选择数值频率(也就是Analytical frequencies选择No)选择Region_1,Scan frequencies in range不勾选,AMS2023以后的版本Hessian选择Auto即可

保存并提交任务。

结果查看

振动谱

点击SCM > Spectra:

Gibbs自由能

SCM → Output → Other Properties → Statistical Thermo Analysis,可以看到相关自由能信息(默认是 298.15K,1 atm大气压,如果需要更改温度压强,计算前应该在AMSinput → Properties → Thermodynamics中输入温度、压强),例如:

 Statistical Thermal Analysis  ***  ideal gas assumed  ***

  
 Pressure:                  1.000000 atm.
 Temperature:             298.150000 K



 Moments of Inertia [amu*bohr^2] and principal axis
 ==================================================

          10.3691        108.0343        112.6403
 ------------------------------------------------
           0.8114          0.5107          0.2845
          -0.5809          0.7584          0.2954
           0.0649          0.4050         -0.9120


 The rotational contribution to the molecular entropy includes
 a term, dependent on the symmetry number sigma. The results 
 reported below were computed using sigma = 1, determined from
 the point group symmetry of the input geometry (NOSYM). 
 If this is not the correct symmetry, try symmetrizing the molecule before
 running the calculation (note: linear molecules should be aligned along one
 of the Cartesian axes).
 Contributions from frequencies below 20 1/cm are not included in vibrational sums.
 Their contributions, if any, are reported separately.


     Temp                                                        Transl      Rotat     Vibrat     Total
     ----                                                        ------      -----     ------     -----

     298.15   Entropy (cal/mol-K):                               36.674     19.473      0.495     56.642
              Nuclear Internal Energy (kcal/mol):                 0.889      0.889     15.556     17.333
              Constant Volume Heat Capacity (cal/mol-K):          2.981      2.981      1.461      7.422
          (c) Constant Volume Heat Capacity (cal/mol-K):          2.981      2.981      1.461      7.422

       Summary of energy terms
                                                   hartree              eV         kcal/mol           kJ/mol
                                      --------------------     -----------       ----------      -----------
      Energy from Engine:               -0.881576364380499        -23.9889          -553.20         -2314.58
      Nuclear Internal Energy:           0.027622317856585          0.7516            17.33            72.52
  (c) Nuclear Internal Energy:           0.027621417359811          0.7516            17.33            72.52
      Internal Energy U:                -0.853954046523914        -23.2373          -535.86         -2242.06
      pV/n = RT:                         0.000944186013486          0.0257             0.59             2.48
      Enthalpy H:                       -0.853009860510428        -23.2116          -535.27         -2239.58
      -T*S:                             -0.026912637077881         -0.7323           -16.89           -70.66
  (c) -T*S:                             -0.026912823599145         -0.7323           -16.89           -70.66
      Gibbs free energy:                -0.879922497588308        -23.9439          -552.16         -2310.24

Gibbs自由能为 -552.16 kcal/mol