AOMix | AOMix-FO | FAQ | SWizard
A shortcut to FAQs about AOMix-FO
If you have a question about the software and you cannot find an answer for it in the program manual and this website, please e-mail your question to S. Gorelsky. If the question is of general interest, the answer will be posted on this page (instead of an e-mail message reply to you).
Q: I use a non-English version (for example: Japanese, Chinese, or Korean) of Windows 2000 / XP. What should I do to run the programs on my computer?
Before starting the program, switch your computer to the US keyboard (type the command US in the Windows command prompt).
Q: Our group/institution has purchased the AOMix license. Will it be possible to organize the AOMix software workshop at our site?
Yes, it will be possible to have a local AOMix software workshop. Please contact the author for scheduling and other relevant details.
Q: Does AOMix use any network connectivity?
AOMix does not use any network connectivity.
Q: Can AOMix and its modules be combined with output files produced by Linux versions of Gaussian 98, GAMESS, etc.?
All the programs on this website will work with output files no matter which was the original operating system. For example, I run my computational jobs on a PC Linux cluster and I run AOMix on my laptop computer under Windows XP.
Q: I have output files from a quantum-chemical software which currently is not included in the AOMix supported software list. What should I do?
Please collect four output files from your quantum-chemical software package:
these files should contain LCAO-MO coefficients and, if it is a HF or DFT calculation, the overlap matrix. Please create a zip or rar file containing these four output files, also please include corresponding input files.
Q: What if I have a problem running the software?
The software has many built-in error checks. If you encounter a problem, please
If you have tried to run your calculation with the most recent version and still have a problem, please send an e-mail (email@example.com) with a description of your problem. In your e-mail, indicate
C:\AOMix\> dir > folder-list.txt
Q: What should I do to visualize the Mayer bond orders (calculated by AOMix) in UCSF Chimera?
Follow these steps:
You can edit the AOMix-atom-chimera2.txt file before importing its data to UCSF Chimera to suit your needs:
Use the PSEUDOBONDS keyword in aomixpar.txt to change the default print format, threshold value and color for PseudoBond attribute files.
You can change atomic/background colors and atomic and bond rendering by using the standard Chimera commands. Please refer to the UCSF Chimera manual for further instructions.
Q: How much time does it take to run an AOMix-FO calculation for a molecule containing 50 atoms?
Approximately 5 minutes on any modern destop or laptop computer. All CPU-intensive modules of AOMix are written in Fortran for fast execution. Here are a few examples (using a laptop computer with a Pentium IV mobile 1.7 GHz processor, 256MB RAM and MS Windows XP as an operating system):
Spin-restricted calculations will take ~50% less time than spin-unrestricted calculations.
Q: I am interested to evaluate back-donation in Pt-CO clusters. Can AOMix provide occupation numbers for 2pi* orbitals of the CO ligands in the clusters?
yes, an AOMix-FO output file contains occupation numbers of fragment molecular orbitals, such as 2pi* orbitals of the CO ligands in the Pt-CO clusters. Thus, you can use AOMix for the analysis of the back-donation in the Pt-CO clusters.
Q: Does the AOMix program work with applied external field in Gaussian (e.g., "FIELD" or "CHARGE" keywords)? For example, the orbital interaction diagrams?
yes, AOMix can process calculations with applied external field. This includes orbital interaction diagram calculations.
Q: In one of the AOMix-FO calculations, we are getting a small but negative backdonation. Does it constitute a red flag meaning something is procedurally wrong? I believe I've actually seen a couple of examples from Frenking where he had a negative backdonations (BH3-NH3 off the top of my head). If it's ok, what is the physical meaning of the negative sign?
yes, negative electron donation and backdonation numbers (they are usually small and do not exceed -0.02) do come up from time to time, especially if the basis set with duffuse functions is employed in calculations. These negative values are artifacts of the Mulliken population analysis and have, of course, no physical meaning. It is safe to assume that those numbers are just zeros.
Q: I have two different molecules, one of them is X and the other one is X with a gold cluster attached to it. I want to calculate the overlap of molecular orbitals which belong to these two different molecules. The idea is to pick up the orbitals which resemble the most. For example, if I pick up orbital number 47 from the first gaussian output, I wanna calculate the overlap of this orbital with all the orbitals from the second gaussian output. Can I do this with your program?
yes, AOMix-FO can map molecular orbitals of molecule X with molecular orbitals of complex XY. The overlap between the molecular orbital #47 of X and the molecular orbital #N of XY will be equal to a percentage contribution (devided by 100%) from orbital #47 of molecule X to the molecular orbital #N. This information is available from AOMix-FO output files.
Q: We are going to calculate the MO compositions of a molecule containing a metal atom using AOMix after finishing a single-point calculation by Gaussian 03.
977 106 Sm 1S 978 1PX 979 1PY 980 1PZ 981 2S 982 2PX 983 2PY 984 2PZ 985 3S 986 3PX 987 3PY 988 3PZ 989 4S 990 4PX 991 4PY 992 4PZ 993 5D 0 994 5D+1 995 5D-1 996 5D+2 997 5D-2 998 6D 0 999 6D+1 *** 6D-1 *** 6D+2 *** 6D-2 *** 7F 0 *** 7F+1 *** 7F-1 *** 7F+2 *** 7F-2 *** 7F+3 *** 7F-3 *** 8F 0 *** 8F+1 *** 8F-1 *** 8F+2 *** 8F-2 *** 8F+3 *** 8F-3
The electron configuration of Sm(II) is [Xe]4f6 5d0 6s0. We are interested to calculate the populations of "real" 4f, 5d and 6s atomic orbitals of Sm(II) in the whole molecule. How to accomplish this?
The easiest way to relate the 1S, 1PX, ......, 8F-3 basis functions to the "real" atomic orbitals, including valence 4f, 5d and 6s orbitals, is to perform the AOMix calculation in which the whole molecule in separated into the Sm(II) ion fragment (an isolated ion) and the rest of the molecule as the second fragment. This calculation will allow you to get the "real" atomic orbitals of the metal ion as fragment orbitals and the AOMix-FO output file will report their populations in the complex.
Q: I have done some calculations on metal-olefin complexes with Gaussian 03W program using the LANL2DZ basis set for the metal and 6-31G(d) for the rest of the atoms but when I tried to run AOMix I get the ERROR 5 message. On the other hand if I use the same basis set for all atoms AOMix terminates normally. Is there a way to run AOMix using mixed basis sets?
AOMix can process calculations with mixed basis sets (the GEN keyword in Gaussian) but you need to ensure that the number of d orbitals in each shell (five vs. six) remains the same in the whole molecule and fragment calculations. In Gaussian, this can be done by using the 5D keyword for calculations with five d functions (pure d functions) and the the 6D keyword for calculations with six d functions (Cartesian d functions) per shell. When using the Gen keyword, the basis set explicitly specified in the route section always determines the default form of the basis functions.
Doing back to your example, the 6-31G(d) basis set uses Cartesian d functions by default. The LANL2DZ basis set uses pure d functions by default. If you use a mixed basis set such as LANL2DZ for metal and 6-31G(d) for the rest of the atoms, Gaussian will run a whole molecule calculation using pure d functions. If you forget to include the 5D keyword for the olefin fragment, this fragment calculation will be done using Cartesian d orbitals. Thus, the number of orbitals in the whole molecule will be less than the sum of the numbers of fragment orbitals and AOMIx-FO will terminate giving you the ERROR 5 message.
The following example shows how to setup Gaussian calculations for the AOMix-FO analysis of the Fe(CO)4(C2H4) complex (with Fe(CO)4 and C2H4 as fragments) when using a mixed TZVP/6-31G(d) basis set (TZVP for Fe and 6-31G(d) for the other atoms) with pure d functions:
-------- the input file for the Fe(CO)4(C2H4) ------- #P B3LYP/GEN 5D SCF=Tight Pop=Full IOp(3/33=1) The Fe(CO)4(C2H4) complex, the molecule is in standard orientation (NOSYMM is not needed) 0 1 Fe 0.000000 0.000000 0.018179 C 1.821462 0.000000 0.090291 C -1.821462 0.000000 0.090291 C 0.000000 1.503897 -0.976361 C 0.000000 -1.503897 -0.976361 O 0.000000 2.460510 -1.620978 O 0.000000 -2.460510 -1.620978 O -2.968878 0.000000 0.160975 O 2.968878 0.000000 0.160975 C 0.000000 -0.704147 2.039071 C 0.000000 0.704147 2.039071 H 0.910796 -1.252234 2.262845 H 0.910796 1.252234 2.262845 H -0.910796 1.252234 2.262845 H -0.910796 -1.252234 2.262845 Fe 0 TZVP **** O C H 0 6-31G(d) **** ----- the input file for Fragment 1 ----- #P B3LYP/GEN 5D SCF=Tight Pop=Full IOp(3/33=1) NOSYMM Fragment 1, Fe(CO)4 0 1 Fe 0.000000 0.000000 0.018179 C 1.821462 0.000000 0.090291 C -1.821462 0.000000 0.090291 C 0.000000 1.503897 -0.976361 C 0.000000 -1.503897 -0.976361 O 0.000000 2.460510 -1.620978 O 0.000000 -2.460510 -1.620978 O -2.968878 0.000000 0.160975 O 2.968878 0.000000 0.160975 Fe 0 TZVP **** O C 0 6-31G(d) **** ----- the input file for Fragment 2 ----- #P B3LYP/6-31G(d) 5D SCF=Tight Pop=Full IOp(3/33=1) NOSYMM Fragment 2, C2H4 0 1 C 0.000000 -0.704147 2.039071 C 0.000000 0.704147 2.039071 H 0.910796 -1.252234 2.262845 H 0.910796 1.252234 2.262845 H -0.910796 1.252234 2.262845 H -0.910796 -1.252234 2.262845