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Tutorial for GAMESS-US on VigyaanCD

This tutorial describes preparation and optimization of acetic acid dimer using Ghemical and GAMESS-US available on VigyaanCD. The basic idea of this tutorial is to create a starting structure for the system, using the Ghemical-GMS interface and prepare an input file for GAMESS-US. The job is submitted using GTK-GAMESS. The optimized structure is converted to XYZ format using 'babel' and visualized using Jmol.


Acetic acid dimer

1. Open Ghemical-GMS using the desktop icon.
2. Start a molecular mechanics (MM) project [see Figure 1]
3. Choose Draw tool to start drawing molecular structure [see Figure 2]
4. Draw C-C bonds (C is the default atom) for the two acetic acid molecules [see Figure 3]
5. Change the atom type to Oxygen [see Figure 3 and see Figure 4]
6. Draw the O atoms [see Figure 5]
7. Rotate the molecule out of plane [see Figure 5]. This step is required to break the planarity of the system. If the system is completely planar, it may cause problems in optimization.
8. Draw H [see Figure 6]. See step 5 to change the atom type.
9. Start the GAMESS input preparation interface [see Figure 7]. Right click -> Compute -> Gamess input
10. Click on the General tab and choose calculate=Equilibrim Geometry [see Figure 8]
11.Choose with=PM3, this is the level of theory for calculations [see Figure 9]. PM3 is a semi-empirical level of theory
12. Click on Review to overview the input file [see Figure 10]
13. Type is the following lines after line starting with $SYSTEM
     $STATPT NSTEP=200 $END
     $SCF DIIS=.T. $END
(see Figure 11)
14. Click on keep and then save the file (e.g. dimer.inp) [see Figure 12]
15. Start the GTK-GAMESS (Start -> GAMESS -> GTK-GAMESS) interface for job submission
16. Choose the input file; File -> New [see Figure 13]
17. Start the job [see Figure 14]
18. After the job is complete, we can convert the optimized structure to XYZ format using babel [see Figure 15]
19. Start jmol [see Figure 15]
20. Visualize the unoptimized (dimer.log) and optimized (dimer_opt.xyz) structure [see Figure 16]

Note: Jmol displays the first structure in a GAMESS output file.

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Content owner: Pratul K. Agarwal, agarwalpk_AT_ornl.gov
URL http://www.vigyaanCD.org/gamess/ghemical-gms-tutorial-dimer.html
Updated: Thursday, 14-Dec-06 14:38:39 PST
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