Troubleshooting Guide and Tips
Tips:
- Have your home directory in your Finder favorites bar. This will make it easier to find important files. You can do this by going to Finder-->Go-->Home and then dragging the home icon to the favorites sidebar.
- Don't leave all your files in downloads. Put them in your home directory and if necessary, make a folder for a certain project, this will make your computer neater and will help you find files that are exclusive to certain projects.
- If a pathway or a file name is long but unique or partially unique, you can use the tab key to autocomplete the rest. If there are multiple files that fit the bill, you may hit CTRL-D to get a list of matching files.
- If you make a typographical error in a long command, you can hit the up arrow key to bring it back previous commands. Now you may edit your previous commands using CTRL-F (forward), CTRL-B (backwards), CTRL-E (end of line), CTRL-A (beginning of line).
- When using enerCHARMM and an excess (positive) charge is present, you will need to cancel this out with chlorine ions. Make sure you enter the same number given from enerCHARMM into the CLA: part of the next command!
Troubleshooting:
It is important to distinguish between the three common terminal windows you might have open at once. First, a regular OS X "Terminal". This is used to move files around, run system commands (including NAMD), and essentially use much like you would use the Finder.
Next, the VMD Console. This is mostly for VMD to send you messages. It is very uncommon to need to enter any commands here.
Finally, the tkConsole or "tkcon" from VMD. This is used to send commands directly to VMD, using the tcl/tk language ("scripting"). This tkcon uses many of the terminal/shell features you are used to, such as the up arrow to recall commands, and so on. You cannot send system commands via the tkcon, however.
Code won't work? Make sure you aren't in tkcon when you should be in the terminal or vice versa!
No such file found? Make sure you are in the right directory and or the file is in that directory, otherwise the computer wont be able to find the file!
Having issues using tkcon to load a molecule? Try loading it via the VMD menu!
Not sure if a command process is taking a long time or failed? Open up the activity monitor on your mac and see if the process is running or not.
PSF and PDB files not working? Make sure you load the PDB into the PSF, and not vice-versa.
If you are having issues scripting in tkcon, try looking in the VMD menus. It may have a non scripting way to get the job done.
enerCHARMM not working? Make sure the molecule you are using is solvated!
Helpful commands:
ls - This command lists all files and folders within your current directory.
ls -l - This variation of ls will show you your directories and files in a list format
cd - when followed by a directory, it will put you into that directory. If followed by "//" it will put you back into the larger directory that holds the directory you were in. Just cd will put you into your home folder
CTRL-C - pressing the control button and "C" at the same time will end a process.
CTRL-Z - pressing control and "Z" will suspend a command process
fg -this will restart a suspended process
bg -this will run a process in the background
sudo -this makes you run a command as a "super user" this is useful if you Mac is not allowing you to run a certain command because of certain access restrictions. It will require you to enter your password
!! - this is a shortcut to re-enter a command you just used. Easier than copying and pasting sometimes!
$ - if this is entered, then the computer will give you the value of everything after.
top -this is similar to using the activity monitor. If you want to use it, open another terminal to put it in so it doesn't flood your current terminal with information.
history -allows you to see what commands you have done and the time they were used. Useful if you forgot a certain command that you usually don't use or can't find again.
VIM:
vimtutor : starts vim editing a copy of a tutorial file -- very good.
i : insert mode. Next keys typed are inserted into the file.
Esc : Escape from insert mode so you can navigate and use edit commands (stop selecting)
h j k l : move cursor ( h: ← j: ↓ k: ↑ l: → )
A : Append at end of line
o : Insert at new line below
u : undo last command, again and again
x : delete character under cursor
dw : delete everything right from the cursor to the start of next word (and put it into the default register)
dd : delete line (and put it into the default register)
p : paste the default register
/myname : search forward for myname
:wq : write and quit
:x : write and quit
:w filename : write a copy of the file you are editing as filename
:q! : quit without saving even if changes were made!
:help : display help
Tab : use tab completion to scroll through commands that start with what you typed This is used in many programs and shells!
VMD:
http://www.ks.uiuc.edu/Training/TutorialsOverview/vmd/tutorial-html/node4.html
http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.3/ug/node105.html
Linux:
https://ryanstutorials.net/linuxtutorial/navigation.php
http://linuxcommand.org/lc3_wss0010.php
Perl:
https://www.tutorialspoint.com/perl/perl_regular_expressions.htm
C Shell (csh)
https://www.ibm.com/support/knowledgecenter/en/ssw_aix_71/com.ibm.aix.osdevice/c_builtin_cmd_list.htm
VMD Course:
http://copwebsrv.serv.pacific.edu/mmccallu/181
Titin information:
https://en.wikipedia.org/wiki/Titin
VIM Commands:
http://vim.wikia.com/wiki/Best_Vim_Tips