You only need to do this once and executable files are green in MobaXterm. It is important to ensure that the _g16 file is executable by doing chmod +x _g16. # cpu default is 4 memory default is 8GB)Įcho " -> !!!!! does not exist !!!!! "Ĭpulist=`grep Cpus_allowed_list: /proc/self/status | awk ''`Įcho "%CPU=$cpulist" > \$PBS_JOBFS/\$INPUT.gjfĬat \$INPUT.gjf > \$PBS_JOBFS/\$INPUT.gjfĮcho " -> Job submitted! $CPU cpus $MEM mem running $TIME hrs" gjf extension time in hrs otherwise default is 24 hrs Use the script _g16 to run the benzene.gjf job. Personally, I prefer nano:Ĭopy and paste over the lines in benzne.gjf you saved in your editor to MobaXterm (just do a right click). 
To edit a new file in the bash you can either use nano or vi.
You should instead name them as ‘proj_1’ or simply ‘proj1’
Note: your project name or files must never have spaces or special chars between them like ‘proj 1’ or ‘proj&1’. Your calculations will be placed in this project folder and whenever you run jobs wish to view them jobs you can CD:. Change directory (CD) to zl12 project folder:. If this is your first time setting up in Gadi, you will need to setup your own folder:. After the xyz leave 2 blank lines - this is important!. 0 1 – refers to 0 as the charge (this is a neutral structure) and 1 as the spin multiplicity. Important: note the one black space after the keywords and one blank space after If you’re doing potential energy surface (PES) the atoms need to be in z-matrix format. If you are calculating a transition state:. Add the optimization for minimum structure optimization:. Add %nprocshared=4 (to request 4 cpus in a node. Add %mem=8GB (To request 8GB memory in a node. Rename the %chk to benzene.chk (this is checkpoint file). Here are the edits you need to do on your raw gjf file in notepad++:. Another way of organising the atoms’ 3D information is the z-matrix format which we use to do PES scans. You can see the xyz cartesian coordinates of the atoms above. If it prompts you to Submit the job into Gaussian click ‘No’.īefore sending the job to run in Gadi, you need to edit the benzene.gjf file with Notepad++. Then click on ‘Submit’, and save the file as. Untick the ‘Write Connectivity’ and ‘Write PBD Data’ options but keep the ‘Write Cartesians’. 
In the Setup panel click on ‘General’ tab: To do so, once you’ve loaded bezene.pdb in GV, go to >Calculate>Gaussian Calculation Setup… pdb formats if you are using IQ.įor.pdb files you will need to open using GV, export and save it as the gaussian input file format. Once done, save the file into format that can be read by GV, i.e.xyz or. It is highly recommended that you read the guide for these programs too. Iqmol (IQ) is a free software and you can download from here. You can use any molecular GUI available like GaussView (GV), Iqmol, Spartan or even Avogadro to construct your structure.Scp For more information on Gadi and useful basic commands on Linux: In Mac you can also use the Terminal (similar to Linux environment) to transfer files between your computer and NCI’s Gadi, see tips here.
I use WinSCP and for Mac there is Filezilla or Cyberduck. The next step is to acquire a File Transfer Protocol (FTP) client for downloading and uploading files into or from Gadi.If you are using Mac you can remotely access using the terminal. MobaXterm is quite powerful as it can access GUI software like GaussView or VMD from Gadi using Xterm. MobaXterm is great on Windows and I think it should be installable for Mac. To first access Gadi, you need to install your preferred remote access tool.This guide will serve to help you do simple DFT calculations with the Gaussian software, a popular tool for quantum chemical calculations, in the NCI Gadi system.
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