Computational chemistry programs typically read the input file to obtain keywords that tell what should be calculated. In most cases, the molecular structure (the Z-matrix or XYZ coordinates) is given in the same input file after the key words. The organization of the input and the keywords are highly program specific. In case of Gaussian, the relevant input for optimisation of the ground state on N,N-dimethylformamide in few minutes using moderate amount of resources is given below. Insert the following at the beginning of your file using text editor (vi or jot):
%NProc=1 %Mem=32MW %Chk=dmf_min.chk # HF/6-31G(d) Opt=CalcFC MaxDisk=512MW N,N-dimethylformamide minimization 0 1
Inspect your file and save it. A typical Gaussian input file will have a section that allocates computational resources (Link 0 commands that start with %) followed by the route section (lines that start with #), the title section (free format text), and molecule specification (starting with molecular charge and ending with definition of molecular geometry, i.e. Z-matrix). There are three blank lines: one separating the route section from the title section, the other separating the title section from the molecule specifications, and the last one at the end of the molecule specification. The section that you added tells the Gaussian program to allocate 32 megawords (224 MB) of memory and perform optimisation while evaluating the second derivatives at the first point. It also specifies the charge (0) and spin multiplicity (1) for the molecule. Both the charge and the spin multiplicity are integers. Charge is the total charge of the system (e.g. zero for a zwitterionic amino acid) and the multiplicity is 1 for closed-shell molecules in the ground electronic state. Multiplicity is 2 for single radicals and 3 for diradicals, such as molecular oxygen.
To submit the job, issue the command g09 < dmf_min.dat > dmf_min.out & and proceed to the next step.
Prepare the input file for the transition state using Molden. You may start with the ground state structure and rotate the dihedral angle around the N-C(O) bond to be perpendicular with the plane defined by the nitrogen atom and its free attached groups. Save this Z-matrix as dmf_ts.dat and edit it appropriately. As this is transition state optimization, the appropriate input directive is:
%NProc=1 %Mem=32MW %Chk=dmf_ts.chk # HF/6-31G(d) Opt=(TS,CalcFC,NoEigenTest) MaxDisk=512MW N,N-dimethylformamide transition state search 0 1
Submit this calculation locally or on the compute node.
The previous calculations should have produced the optimized geometries for the ground state and the transtion state of N,N-dimethylformamide. However, the optimization jobs did not evaluate partition functions. We need to run a second pair of calculations that evaluate the partition functions, enthalpies, entropies, and free energies for the ground state.
Create an input file for the ground state frequency calculation (dmf_min_freq.dat) that has only the lines shown below. You do not need to copy the Z-matriz because the optimized structure is automatically obtained from the checkpoint file that you specifies in with the %Chk Link 0 command.
%NProc=1 %Mem=32MW %Chk=dmf_min.chk # HF/6-31G(d) Freq=NoRaman Guess=Check Geom=Check MaxDisk=512MW N,N-dimethylformamide minimum 0 1
Create an input file for the transition state frequency calculation (dmf_ts_freq.dat) that has only these lines.
%NProc=1 %Mem=32MW %Chk=dmf_ts.chk # HF/6-31G(d) Freq=NoRaman Guess=Check Geom=Check MaxDisk=512MW N,N-dimethylformamide transition state search 0 1
Submit these calculations.