MCC Summer School
May 29, 2001
This lab will introduce you to the program package NWChem, which is able to perform many different types of quantum chemical calculations and is freely distributed by Pacific Northwest National Laboratory. Feel free to expand on the exercises – a few suggestions for optional calculations are given in case you have time. These exercises emphasize optimization and characterization of local minima and transition states, providing you with the information you would need for computing rates using transition state theory (TST.) We also include some examples of dynamics, as you might use when computing dynamical corrections to TST rates. Online documentation for the NWChem program is available at
http://www.emsl.pnl.gov:2080/docs/nwchem/nwchem.html
The input files for the exercises can be found in the directory ~tjm/mcc.
Running NWCHEM jobs on the NCSA Origin 2000 (Modi)
After logging into modi, find the job you want to run. Change to the directory that the file is in and type:
qnwchem
This invokes the nwchem queue controller. It will ask you for the filename, the number of processors to use (type 1), the queue you would like to submit to (type vst_sj), and the account to be charged (press <return>).
After doing this, you should get a quick message saying the job was submitted. You can check on the status of the job in the queue by using the command bjobs. Although you should not have a need to use it for the exercises given, the command bkill <pid> can be used to remove jobs from the queue once they are submitted. Here <pid> is the job id number listed to the far left in the output of bjobs.
For those jobs that involve a geometry search, you will need to put the final geometry in a PDB file for viewing. To do this, type:
~tjm/mcc/pdbmake
You will be prompted for the NWCHEM output file (the one with the .out suffix) to be read from and the PDB file (.pdb suffix) to write. You will then be prompted for the number of atoms. After this, the PDB file specified will be written. To view the molecule use Rasmol:
~tjm/mcc/rasmol
and open the PDB file using the menubar at the top of the Rasmol window.
This exercise is an energy optimization of a single water molecule. Run the job, and examine the output. What are the bondlengths and angles?
Input file: h2oscfopt.nw
Output file: h2oscfopt.out
2. Water RHF/STO-3G Frequency calculation h2oscffreq.nw
This exercise calculates the normal modes and frequencies of water at the RHF/STO-3G level. Modify the input file to use the geometry you found in 1. Run the job and examine the output. What kind of intramolecular motion does each normal mode characterize?
Input: h2oscffreq.nw
Output: h2oscffreq.out
3. Water RHF/STO-3G Transition State Search h2oscfts.nw
This exercise is a transition state search for a single water molecule at the RHF/STO-3G level. Run the job and examine the output. Of what reaction or intramolecular motion is this the transition state? Examine the bondlengths and angle of this structure in comparison to the equilibrium structure and comment on the differences. Modify the starting geometry and try again – do you always find the same transition state?
Input: h2oscfts.nw
Output: h2oscfts.out
4. Water RHF/STO-3G Transition-State Frequencies h2oscftsfreq.nw
This is a calculation of the normal modes and frequencies at the transition state calculated in the previous exercise. Modify the input file to use the geometry you found in 3. Run the job and examine the output. Identify the motion characterized by the normal modes, and specify which represents the mode with negative curvature. Calculate the height of the barrier at the transition state by subtraction the energy found in 1.
Input: h2oscftsfreq.nw
Output: h2oscftsfreq.outj
5. Water RHF Dynamics h2oscfqmd.nw
This is a simple example of ab initio molecular dynamics in the NVT ensemble at 298K. What is the range over which the angle and bond length vary? Try running at a much higher temperature, e.g. 1000K. How much more do the bond lengths and angles fluctuate?
Input: h2oscfqmd.nw
Output: h2oscfqmd.out
MD Output: h2o_qmd.out
MD Trajectory: h2o_qmd.trj
6. Water DFT/B3LYP/STO-3G Geometry Optimization h2odftopt.nw
This is another energy minimization of water, but this time using density-functional theory with the B3LYP exchange-correlation functional. Run the job and examine the output. What are the values of the geometric parameters (angle and bondlengths) and how do they compare with the structure calculated using RHF?
Input: h2odftopt.nw
Output: h2odftopt.nw
7. Water DFT/B3LYP/STO-3G Frequencies h2odftfreq.nw
This is an analogue of 2. This time calculate the frequencies with DFT. Compare the frequencies obtained with DFT and RHF. Identify the motions represented by the normal modes. Are the frequencies different than those obtained with RHF? Are they systematically higher or lower than the RHF frequencies?
Input: h2odftfreq.nw
Output: h2odftfreq.out
8. Water DFT/B3LYP/STO-3G Transition-State Search h2odftts.nw
Optimize the bending transition state for water using DFT. Compare the resulting geometry with that obtained using RHF. Calculate the barrier height obtained with DFT by subtraction of the minimized energy. How does the barrier height calculated with DFT compare with that calculated using RHF?
Input: h2odftts.nw
Output: h2odftts.out
9. Water DFT/B3LYP/STO-3G Transition State Frequencies h2odfttsfreq.nw
Calculate the frequencies at the bending transition of water using DFT and compare with those obtained using RHF. Are any systematic trends observed in 7. reproduced here?
Input: h2odfttsfreq.nw
Output: h2odfttsfreq.out
10. Water RHF Transition State Dynamics h2oscftsqmd.nw
This calculation provides an example of ab initio molecular dynamics as in 5, but starting from the transition state. First, modify the input file to start from the geometry you found in 9. This is NVT dynamics at 298K. Get a rough estimate of how long it takes to reach the minimum from the transition state.
Input: h2oscftsqmd.nw
Output: h2oscftsqmd.out
MD Output: h2ots_qmd.out
MD Trajectory: h2ots_qmd.trj
11. Water Dimer RHF Geometry Optimization 2h2oscfopt.nw
Optimize a minimum-energy structure of water dimer using RHF. Compare the geometries of the monomers in the dimer to those of the optimized monomers themselves. Measure the distances involved in the hydrogen bond.
Input: 2h2oscfopt.nw
Output: 2h2oscfopt.out
12. Water Dimer RHF frequencies 2h2oscffreq.nw
This exercise calculates the normal modes and frequencies of water dimer at the minimum energy geometry using RHF/STO-3G. First, modify the input file to use the geometry you found in 11. Try to characterize the motion associated with each mode. Compare these to the results for the monomer. Can some or all of the modes of the dimer be identified with modes of the monomers?
Input: 2h2oscffreq.nw
Output: 2h2oscffreq.out
13. Water Dimer RHF Transition-State search 2h2oscfts.nw
Optimize a transition state of water dimer. Characterize the transition state based upon its appearance. What reaction or motion does it represent? Calculate the barrier height energy. Measure the hydrogen-bonding distance and compare to the minimum energy structure. Change the initial geometry and search for a TS again. Do you continue to find the same TS?
Input: 2h2oscfts.nw
Output: 2h2oscfts.out
14. Water Dimer RHF Transition-State Frequencies 2h2oscftsfreq.nw
Calculate the normal modes and frequencies of water dimer using RHF. Modify the input file to use the geometry you found in 13. Relate the frequencies to those of the minimum energy structure where possible. Have analogous modes changed frequency? Are there systematic changes?
Input: 2h2oscftsfreq.nw
Output: 2h2oscftsfreq.out
15. Water Dimer RHF Transition-State Dynamics 2h2oscftsqmd.nw
This calculation provides a further example of ab initio molecular dynamics. First, modify the input file to start from the geometry you found in 13. This is NVT dynamics at 298K. If you are really at a TS, chances should be 50/50 that you will fall to reactant or product. Run a few times and see whether this is what happens. Because reactant and product are chemically identical in this case, you will need to distinguish them by atom numbering – alternatively you could make one of the water molecules HOD, and then reactant and product would be chemically distinguishable.
Input: 2h2oscftsqmd.nw
Output: 2h2oscftsqmd.out
MD Output: 2h2ots_qmd.out
MD Trajectory: 2h2ots_qmd.trj
16. Ethylene MCSCF Energy Minimization ethylenemcscfopt.nw
Optimize the minimum-energy geometry of ethylene using MCSCF (CAS(2/2)).
Input: ethylenemcscfopt.nw
Output: ethylenemcscfopt.out
17. Ethylene MCSCF cis-trans Transition-state search ethylenemcscfts.nw
Optimize the cis-trans isomerization transition state for ethylene using MCSCF. Does it look like you expect it to? Calculate the barrier height of the reaction.
Input: ethylenemcscfts.nw
Output: ethylenemcscfts.out