QwikMD
QwikMD is a user interface that allows for molecular dynamics simulations to be ran with ease. With this ease of use of course, you use some customizability but with an advanced run, we can edit some parts of the simulation.
Open VMD and then go to the Extensions tab and select the Analysis section, then you should see QwikMD pop up as an option. The QwikMD interface should open up and near the top you should see an advanced run tab, select that. The best part about this is plug-in is that you just have to submit a cleaned up PDB and it will solvate it for you if you want it to!
Load in the cleaned up 1qlq molecule you made earlier for the NAMD GUI section, if you do not have it and can't remember how to clean a pdb, click here. You will know the pdb is loaded when you see the molecule load into the VMD window, you can rotate it like any other VMD simulation at the moment.
Explicit solvent is currently the best way to run QwikMD and has the least amount of guessing within the solvation.
Then, click "protocol", a box should then drop down that says Minimization, Annealing, etc. along with a bunch of numbers and other text. The first set of numbers is the number of steps for each process in the MD simulation. We are going to shorten these all steps besides the minimization step by a factor of 100, Annealing will the readjust itself to 2400 as it has to be more steps than the Minimization.
You then have to set up a working directory, you need to do this by clicking the "Prepare" button above the "Start Simulation" button. This will bring up another window for you to select a working directory, you can make one now by just not selecting one and typing a new name into the bar at the top. A bunch of files will then load into this directory and QWIKMD will flash a bit and so will the VMD window, you will see a cube appear around your molecule since we told QwikMD to solvate it.
Click the start button at the bottom and use 4 processors and then click yes, you will not be able to do anything with VMD until the simulation is complete.
Tail -f the log file created to watch it run!
After each step is done, you will have to go back to the QwikMD window to press ok and then start. The entire simulations should take 20-30 minutes.
A DCD file should be the product, a solvated psd was also formed in the very beginning of the QwikMD simulation, load the DCD into this and take a look!