Gaussian manual

However, you can also specify these scale factors explicitly. For a two-layer calculation, the scale factors specify the link atom bond distance in the model system when calculated at the low and high levels respectively. All of these scale factors correspond to the g-factor parameter as defined in reference [ Dapprich99 ], extended to allow separate values for each ONIOM calculation level.

For a two-layer ONIOM, if only one parameter is specified, then both scale factors will use that value. For a three-layer ONIOM, if only one parameter is specified, then all three scale factors will use that value; if only two parameters are specified, then the third scale factor will use the second value.

If a scale parameter is explicitly set to 0. Thus, if you want to change only the second scale factor model system calculated at the medium level , then you must explicitly set the first scale factor to 0. In this case, for a three-layer ONIOM, the third scale factor will have the same value as the second parameter unless it is explicitly assigned a non-zero value i. When only a single value pair is specified, all levels will use those values.

If two pairs of values are included, then the third pair defaults to the same values as in the second pair. If the final pair is omitted for an S-value job, it defaults to the values for the real system at the low level. Thus, when only a subset of the six or nine pairs are specified, the charge and spin multiplicity items default according to the following scheme, where the number in each cell indicates which pair of values applies for that calculation in the corresponding circumstances:.

Use MM charges from the real system in the QM calculations on the model system s. NoEmbedCharge is the default. MKUFF uses the Merz-Kollman-Singh approximate charges during geometry optimization microiterations with electronic embedding but using UFF radii, which are defined for the full periodic table. This is the default.

Specifies that Mulliken approximate charges be used during geometry optimization microiterations with electronic embedding. See Population default method. Specifies scaling parameters for MM charges during electronic embedding in the QM calculations. The integers are multiplied by 0. Atoms bonded to the inner layers use a scale factor of 0.

However, the values of i through n must be monotonically decreasing, and the largest value among them is used for all parameters to its left. Thus, , and are all equivalent. The default value is i. ScaleCharge implies EmbedCharge. Requests that the full square be done for testing, to produce substituent values S-values for the S-value test [ Morokuma01 ]. Additional charge and spin multiplicity pair s may be specified for the additional calculations see below.

Compress operations and storage to active atoms during MO:MM mechanical embedding second derivative calculations; this is the default. NoCompress performs the calculation without compression. Blank does the uncompressed calculation but then discards contributions from inactive atoms which are currently non-zero only for nuclear moment perturbations: shielding and spin-spin coupling tensors.

This is faster for medium-sized systems but uses more disk space for large ones. Be very careful in your atom assignment and in your assignment of charge and multiplicity to the fragments. How the Counterpoise calculation actually works.

During the counterpoise calculation, Gaussian 03 performs 5 separate single point energy SPE calculations at the level specified in the route section. Think D for dimer. Step 3: SPE calculation of fragment 2 using all available orbitals.

This is called. Step 4: SPE calculation of fragment 1 using only orbitals associated with that fragment. This is called an MCBS calculation. Think M for monomer. Step 5: SPE calculation of fragment 2 using only its own orbitals. Counterpoise corrected energy is simply the sum of the original electronic energy calculated in Step1 and the BSSE correction.

Deciphering Counterpoise Calculation Output. Three kinds of data can be found in the output for calculations of this type. If you have any concerns about your counterpoise correction you can record each value. If they are not similar, you may have missassigned the atoms to the respective fragments. For whatever reason, this missassignment can wreak havok with the calculated counterpoise correction.

An example of BSSE estimation using the counterpoise method:. To correct for this error, we perform a counterpoise calculation. Counterpoise correction: 0. Note that as the basis set increases in size, the basis set superposition error should decrease by definition.

By extension, the magnitude of the counterpoise correction should also decrease. This can be seen from a study of alkylation of dimethylacetamide enolate anion by methyl chloride. Table 1. Effect of basis set on B3LYP relative electronic energies for the reaction of dimethylacetamide enolate anion and Methyl Chloridea G d reactant complex IRC calculations allow you to follow a reaction from the transition structure to the reactant or reactant complex , and from the transition structure to the product or product complex.

Thus to map out the entire reaction coordinate you will need to run two IRC calculations arbitrarily designated as forward and reverse , starting from the same transition structure. Thus the first job is to get the transition structure. Once this is obtained it is easy to. So in this example I have taken an enolate alkylation transition structure h , copied its checkpoint file to h Note that a priori one does not know which "way" a "forward" IRC calculation will proceed from the transition structure.

However, in this case, the "forward" IRC calculation did go to the intended products. In my experience the most critical factor for success in IRC calculations is setting the step size. You have to play with this. If the step size is too big, I have seen at least two unwanted things happen 1 you won't seem to progress along the reaction coordinatethis is confusing, because you will think you need to further increase the step sizewhich is tragically deceptive.

For example, in the present case with a stepsize of 10, this IRC runs smoothly in the forward and reverse directions. With a stepsize of 50, this IRC runs only in the forward direction and the first point is UP in energy from the transition structure.

It will not go anywhere productive in the backward direction with this large stepsize, even if the phase is specified bond axis for movement. With a step size of 25, it runs in the forward direction, but again the energy of the first step is UP not as much as when it was In both the cases of 50 and 25, the forward IRC gets close to the product, but a vibrating behavior is seen and a stationary point is never reached.

An attempt at running the backward IRC with a step size of leads to a vibration, and an explosion. However, in the case of stepsize of 10, the forward and backward IRC go smoothly 20 points towards the product and SM respectively, but never give the message "Minimum found.

Thus although you may be successful at getting the IRC calclulations to proceed towards reactant and product, you may still not be successful at reaching your final destinations "Minimum found". Do not dismay. You must first assess how much progress you have made energetically, and to do this the easiest procedure is to take your points of furthest progress, save these geometries, and initiate geometry optimizations.

These equilibrium geometries and associated energies will tell you how far away your IRC final geometries are from the goal. At this point you may need to restart the IRC calculation.

To restart, you rename the. In this job the first point will be 21 since we ended at 20 in the original calculation , and will terminate at point Note that even then, you may not get to a perfect equilibrium geometry; in my case an oscillating behavior ensued for both forward and reverse IRC calculations.

However, by paying attention to the energies, it is clear that the reverse IRC calculation was very successful at bringing us to the reactant complex. File h h H h h hr h hr hr2 h Calculation enolate CH3Br total sep. As the table shows, the relative energy at the end of hr is What is wrong with the forward IRC calculation, where the furthest point is only Inspection of the structure shows the C-C bond is fully formed and the product is in a good conformation.

However, in this case the product is the alkylated enolate and a bromide ion, and the position of the bromide ion plays a huge role in the energy of the product complex.

This is shown by deleting the bromide from both hr2 and h, and taking single point energies. In this case we showed that the organic fragment of hr2 was only 2. Thus apparently, movement of the bromide to it's favored position is not driven by the same forces that move the IRC from the transition structure towards C-C bond formation.

Monitoring IRC Calculations You must follow what is happening, because failure is common and you don't want to waste your own and everyone else's time. Again, Molden or GaussView3 will provide the easiest way to monitor these calculations.

Visual inspection of geometries and energies is the key. Note that in Molden all one can assess is how many points have. Points are not the same as steps; a step moves you on the reaction coordinate a certain amount governed by stepsize. However after each step is taken a constrained optimization follows, and this may take or or more points. In Molden if one looks at geometric convergence you can often see the energy go down in increments, and the bigger increments most often correspond to these steps.

Note that the first step of an IRC calculation may actually be slightly higher in energy than the TS. Don't abort the IRC calculation too quicklygive it a chance to see if the energy starts going down. Once the number of steps reaches the set maximum the calculation will quit. In the case of h, the IRC calculation terminated normally at the 20th step, even though a minimum was not found. Using the egrep commands listed above on h To see whether the energy is decreasing as desired, the easiest way is to use Molden or GaussView3.

But if you want, you can generate an. See Section 17 below for a description of ircextract2. This will give you the energies at each optimized point, which allows you to see if the energies are decreasing as desired.

To learn whether the calculation has found a stationary point, you need to look for " Minimum found on this side of the potential", so egrep 'Minimum found'. Note that if the final step is calculated, you will get the nice quotation even if the last point is not a stationary point. As mentioned above, you can restart the calculation if you ran out of points, and possibly increase maxpoints.

But even then, as described above, you may not find the stationary point. You need to get the TS from the original optimization. Again, I think that Molden will sometimes be the best way to export structures from an IRC calculation. This can be done by selecting each point of interest, and using the "write" functionality. Nevertheless, there is a command line way to do this, and it is described below. The command line method is at present the best way to get the energies and structures out for the purpose of making a movie.

I am hoping that GaussView4 will make this process easier. Use a script to extract coordinates and energies from these files and store them in an. There are two scripts that will be useful get them from Paul : ircextract. The second is to be used when you have edited gaussian's z-matrix. The syntax is as follows: awk -f ircextract2.

This takes the data from the output file and stores just what you need in an xmol file. Note: to look at the unoptimized geometries Polo created another script to do the same thing--it is optextract. Then use WordPad to create individual.

Open two windows and copy each step into a new. In this case I took data from the. Manually change suffix of all these files to. I have been looking for good renaming programs for Mac. Renamer and R-Name. Still learning these.

This is done using Import and Export commands, obviously. PyMOL can only read pdb files, that is why we are doing this. Can we find another way to go from. Will Molden work? Will newzmat work? Should we write an. Use PyMOL to load all the. Once all of them are loaded, you can turn individual ones off by clicking the button, or type 'disable all' to turn them all off B.

Reorient selected structures, if necessary. Sometimes the coordinate system appears to have changed and the molecules don't overlay correctly. You can then select the first structure and the second structure. Select three pairs in all, and then click the 'Fit 3 pairs' button.

If it looks good, click done. Then turn off the first structure, turn on the third, and fit the third to the second. Be sure to use the same anchor atoms in each case. When you are done, 'Save Session'. You will want to make all the carbons the same color and set your other display options. If you have a bond-breaking TS, at the TS the non-bonded atom may appear as a cross.

Decide on which views you want to start with and move to. For example v1 is far away, v2 is rotated far away and v3 is close up As you get each desired view, type view v1, store then continue for v2, v3, as needed. This is best done in a text editor. The basic command is mvCmd, followed by a frame number, a command, and a filename. Here is the script for my LiNH2 cyclopropyl nitrile deprotonation movie: mvCmd 1, disable ha13 mvCmd 1, enable hr22 mvSinViewTravel , v1, v2 mvSinViewTravel , v2, v3 mvCmd 61, disable hr22 mvCmd 61, enable hr21 mvCmd 62, disable hr21 mvCmd 62, enable hr20 mvCmd 63, disable hr20 mvCmd 63, enable hr19 mvCmd 64, disable hr19 mvCmd 64, enable hr Carlier Group Gaussian User Manual disable hr18 enable hr17 disable hr17 enable hr16 disable hr16 enable hr15 disable hr15 enable hr14 disable hr14 enable hr13 disable hr13 enable hr12 disable hr12 enable hr11 disable hr11 enable hr10 disable hr10 enable hr9 disable hr9 enable hr8 disable hr8 enable hr7 disable hr7 enable hr6 disable hr6 enable hr5 disable hr5 enable hr4 disable hr4 enable hr3 disable hr3 enable hr2 disable hr2 enable hr1 disable hr1 enable ha disable ha enable ha1 disable ha1 enable ha2 disable ha2 enable ha3 disable ha3 enable ha4 disable ha4 enable ha5 disable ha5 enable ha6 disable ha6 enable ha7 disable ha7 enable ha8 disable ha8 enable ha9 disable ha9 enable ha10 disable ha10 enable ha The key thing to remember is that you need to enable and disable individual views, The enabling and disabling is best done in a single frame.

In frame 1 we are disabling the last view so that playback is not compromised , then showing the first view, and beginning a rotation.

The movement from view 1 to view 2 takes place over 30 frames will be 2 seconds , then the movement from view 2 to view 3 takes place over 30 frames. Preview the movie. Copying the text in this script and pasting it into the command line. Hit return and give it a second. Then type movie in the command line, and hit the play triangle on the lower left. Note that you want to clear all extraneous views before doing this. If you like it, great. If you want to make changes, go ahead. This will generate the png files in the PyMOL directory.

Assemble the movie frames into a movie file. Then use VideoMach or Quicktime Pro to create a movie from the. Basically you put all the. You will be prompted for additional parameters, such as frame rate, and whether you want to make a selfcontained movie. Acknowledgements We thank Professors T. Daniel Crawford and Diego Troya for many helpful discussions and suggestions, but we take responsibility for any and all errors, typographical or conceptual.

Appendix 1: Why your calculation failed If Calculation does not start on giving the qsub command: because of a wrong pathway specified in the. Because of the presence of ampersand at the end of nohup command If you see your job queued up: You have specified more memory or processors than currently available, or you have surpassed the number of jobs allowed.

Reason: There is an extra space between your title line and your description 3 End of file in ZSymb. You need to have at least 1 space after geometry specification. Reason: check your charge and multiplicity one of them is wrong!

Reason: There is a problem with convergence during geometry optimization. Reason: This is also a convergence issue, though I have usually seen this occur after a number of cycles usually more than a day of computational time and could also be due to lack of sufficient resources.

Cartesian coordinates read from the checkpoint file: thfer. Reasons: 1. You have specified geometry but have forgotten to put a description. There is an extra line between your command line and description. Appendix 2: Useful awk scripts A. Open navigation menu. Close suggestions Search Search. User Settings. Skip carousel. Carousel Previous. Carousel Next. What is Scribd? Explore Ebooks. Bestsellers Editors' Picks All Ebooks. Explore Audiobooks. Bestsellers Editors' Picks All audiobooks.

Explore Magazines. Editors' Picks All magazines. Explore Podcasts All podcasts. Difficulty Beginner Intermediate Advanced. Explore Documents. Gaussian Manual. Uploaded by Ismail Adewale Olumegbon. Did you find this document useful? Is this content inappropriate? Report this Document. Flag for inappropriate content. Download now. Related titles. Carousel Previous Carousel Next. Jump to Page. Search inside document. Very good reference for Hartree-Fock theory we do not have this book at present: it is available in the library ISBN To use Gaussian successfully on Inferno2, you will need to learn the basics of the Unix operating system.

Text Editors You will need to use a text editor to create and modify your g03 input files, and to search your output files. In command mode, a few helpful commands to get you started are to save your work, type :w to exit if no changes have been made since the last save, type q to exit without saving your work, type :q! Helpful Unix commands To view a file on screen cat filename.

Permissions Note: as described below in 1. This will make the pub directory accessible. Once that group membership is defined, you can change the group classification of your directory by chgrp prc cyclopropyl Now the directory cyclopropyl has a group classification of prc defined below.

Process management Note that Fugu is a Note that you can kill only those processes of which you are the owner! Bash Profile To ensure that you can use all the functionality of g03, you should ensure that your.

When g03 runs a job, Why is there so much information in the header? Getting geometry information for your input file Historically we have used Spartan to build structures, and then moved them to Gaussian. Starting Calculations: 15 Since the introduction of the queuing system, the procedure for starting a calculation on Inferno2 has completely changed. Carlier Group Gaussian User Manual 17 Possible Concerns with Internal Coordinates The g03 manual is quite clear that starting with g03, the format of the initial geometry in the input file is now completely inconsequential, since both cartesian coordinates and Zmatrices will be converted into redundant internal coordinates before the optimization begins.

Converting Z-matrices or Cartesian Coordinates to Enantiomeric Structures To make the enantiomer: change the sign of the dihedral in the Z-matrix, or for cartesian coordinates, change the sign of one of the coordinates for each atom i. Options Note that since geometry optimizations can be so time-consuming it is worthwhile to use the following time-saving techniques i The gdiis option is good for the flat potential surface of DFT.

Multiple Constraints I have had occasion to perform optimizations with one fixed dihedral constraint and one dynamic dihedral constraint. Monitoring constrained optimizations To check conveniently--find out the internal coordinate name for your constraint--this will be R for a bond length, A for an angle, D for a dihedral egrep D37 h Export as pdb and view in Spartan, RasMol, or gOpenMol Use newzmat to generate a pdb file from your checkpoint file: newzmat ichk opdb filename. Visualizing Imaginary Frequencies To do a quick check that your imaginary frequency corresponds to the correct molecular motion, Molden or GaussView4 are the easiest option.

Measuring bond lengths, angles, dihedrals Please note that since coordinates in. Carlier Group Gaussian User Manual Setting up a calculation to obtain thermodynamic parameters Adding the freq keyword to the route section prompts Gaussian to start calculating frequencies and thermodynamic parameters once the geometry is optimized.

To see detailed entropy information, type more h Obtaining thermodynamic parameters at any temperature Gaussian 03 calculates thermodynamic parameters at STP Standard Temperature and Pressure which means Otherwise it will ask you what While this utility is running, a large amount of data starts scrolling by. The Running a Counterpoise calculation In order to correct for the BSSE imposed when calculating clusters of molecular fragments e.

How the Counterpoise calculation actually works During the counterpoise calculation, Gaussian 03 performs 5 separate single point energy SPE calculations at the level specified in the route section. This is called DCBS2. Deciphering Counterpoise Calculation Output Three kinds of data can be found in the output for calculations of this type. Carlier Group Gaussian User Manual 45 IRC Calculations note: this section substantially revised June 25, IRC calculations allow you to follow a reaction from the transition structure to the reactant or reactant complex , and from the transition structure to the product or product complex.

To learn whether the calculation has found a stationary point, you need to look for " Minimum found on this side of the potential", so egrep 'Minimum found' Note that if the final step is calculated, you will get the nice quotation even if the last point is not a stationary point.

Carlier Group Gaussian User Manual 49 Reorient selected structures, if necessary Sometimes the coordinate system appears to have changed and the molecules don't overlay correctly. Select your display options 51 You will want to make all the carbons the same color and set your other display options. Decide on resolution normally x Polo recommends the following viewport , set orthoscopic this command makes the display and ray tracing programs adopt the same perspective E. Decide on which views you want to start with and move to For example v1 is far away, v2 is rotated far away and v3 is close up As you get each desired view, type view v1, store then continue for v2, v3, as needed.

Then use scripts to generate an animation and change viewing options. Preview the movie Copying the text in this script and pasting it into the command line. Make your movie frames. Assemble the movie frames into a movie file Then use VideoMach or Quicktime Pro to create a movie from the. Documents Similar To Gaussian Manual. Sachin Tyagi. Dan Mark Pidor Bagsican.

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Link 0 commands were introduced in the last chapter and are discussed individually in the penultimate section of this chapter. The remaining input sections are discussed in the subsequent subsections of this introductory section.

For convenience, the table below lists all possible sections that might appear within a Gaussian 03 input file, along with the keywords associated with each one. Spaces, tabs, commas, or forward slashes can be used in any combination to separate items within a line. Multiple spaces are treated as a single delimiter. Multiple options are enclosed in parentheses and separated by any valid delimiter commas are conventional and are shown above.

All keywords and options may be shortened to their shortest unique abbreviation within the entire Gaussian 03 system. Thus, the Conventional option to the SCF keyword may be abbreviated to Conven , but not to Conv due to the presence of the Convergence option. This holds true whether or not both Conventional and Convergence happen to be valid options for any given keyword.