Author Archives: Charles Clayton

Decoding: AMBER code

In a previous blog post, I presented a code I used in AMBER to run a trajectory of a protein. The code is below:

nohup mpirun -np 4 sander.MPI -O -i mdin -p -c 3beq.crd -r 3beq_md.crd -x md.trj -o md.out &

Before you can run code successfully, you have to know what the code means and how to set up the code. The code above contains flags and the files you need to run the simulation. The flags precede the files that contribute to the flags. The flags are the individual letters with the dash in front of them.


  • -O: overwrites any output file with the same name
  • -i: input file
  • -p: parmtop file
  • -c: coordinate file
  • -r: restart file (output of new coordinates)
  • -x: trajectory file
  • -o: output file
  • -np: specifies the number of processors
  • -ref: reference file [Not in code above, but used in other codes]

Other than the flags and files, there are commands that also contribute to the running of the code. The command nohup and & are used. As previously discussed, nohup allows codes to run without hanging up and & allows codes to run in the background. So together, nohup and &, allows you to logout of comet or continue doing other things on comet while your job runs. A new command that is present in the code is mpirun, which cause the code to be executed in parallel.

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Using Vi/Vim

Vi and Vim are ultimately the same thing. Vim is just the improved version of Vi. Vi/Vim is a text editor that is used in PuTTY when using comet.

Vim is needed when running molecular dynamics simulations because it allows you to quickly edit files and check results in output files. But, Vim isn’t your average text editor. Since it is designed for software like PuTTY, it makes editing very easy. The easy editing and the ability to edit your files in any way makes Vim very powerful.

Vim has many commands that contribute to how powerful the text editor is. Some of the helpful commands in Vim are :wq, i, u, G, gg, and :help cmd. Command, :wq, saves all the edits you have done to the file. Command, i, enables insert mode, which allows you to insert and delete things. Command, u, undoes previous action. Command, G, moves to the  end of the file. Command, gg, moves to the beginning of the file. Command, :help cmd, gives you help about whatever cmd is. cmd can be anything you need help with.

One amazing thing about Vim that is helpful and essential is vimtutor. Vimtutor is a multi-lesson tutorial on how to use and gives you important commands to use Vim. Each lesson have many parts to it. If you go through the entire tutorial, you will be about to effectively use Vim. There is a learning curve though. It takes a while to get use to, but after practice with Vim and using Vim, you’ll be a pro.


Above is the beginning of vimtutor.



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Accessing and Using Comet

Comet is the super computer center in San Diego that I’m using to run molecular dynamics simulations. In order to use the super computer in San Diego on your local computer, you have to use a ssh client and a scp client. Since I am wirking on a Windows computer, the ssh client I used was PuTTY and the scp client I used was WinSCP. There are different programs to use on other operating systems. All you have to do is sign into your comet account on PuTTY and WinSCP, and you have access to the things in your comet account and the super computer.

The ssh client, PuTTY, is the program that allows you to communicate directly to the super computer. PuTTY on your local computer connects the remote computer, comet. When you are typing in and navigating PuTTY, you are typing in and navigating comet. The actual molecular dynamics simulations are done in PuTTY.

The scp client, WinSCP, is the program that allows you to transfer files from comet to your local computer. You can easily transfer files back and forth, from local to emote computer in a short period of time.

To learn how to use comet, I had to learn how to use PuTTY and WinSCP. Also, I needed to learn basic linux commands because in PuTTY you use linux commands to control comet. Linux commands like mkdir, cd, cp, mv, and ls are really essential and used a lot. mkdir creates a directory, cd changes the directory, cp copies files, mv moves files, and ls lists the files in the current directory. I think the nohup command followed by the & at the end of job was most useful so far because it allows jobs to run in the background without hanging up. This allows you to run other jobs or do other things without stopping the job. WinSCP can be used like any other file manager program, no linux commands needed.

An example of the nohup command to run a trajectory:
nohup mpirun -np 4 sander.MPI -O -i mdin -p -c 3beq.crd -r 3beq_md.crd -x md.trj -o md.out &

Comet allows me access to AMBER, which lets me use tleap, sander, and cpptraj. Those are programs are essential to running molecular dynamics.

PuTTY and WinSCP

Comet is the black screen on the left and WinSCP is the left screen.


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Molecular Dynamics Simulation Process and AMBER

I learned the Molecular Dynamics Simulation process by dealing with the protein Influenza Neuraminidase 3BEQ. Molecular Dynamics Simulation is a multi-step process.

First, I had to visit the protein data bank to download the protein Influenza Neuraminidase and put in a directory on comet. Second, I had to setup the protein in tleap in AMBER. While I set up the protein in tleap, I had to add Ions to the protein and solvate the system with a water box. Third, you have to save the protein in a coordinate and topology file. Fourth,  I needed to run energy minimizations using sander in AMBER. Fifth, I then needed to run equilibration. Sixth, I had to run a molecular dynamics run. Seventh, I had to use cpptraj to run a trajectory analysis. Lastly, I used VMD to view the simulation.

The process is tedious and allows a lot of place for error and typos, which could be annoying. Aside for the errors that could take place, the molecular dynamics simulation process is not too bad to handle with guidance.



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Using Putty and WinSCP to run molecular dynamics simulations on Influenza Neuraminidase 3BEQ

I first had to run a molecular dynamics simulation (via. workshop 1) to visualize the protein Influenza Neuraminidase 3BEQ. But before you can run a molecular dynamics simulation, you must know how to set up the simulation. Setting up the simulation and running the simulation wasn’t too bad. There is a learning curve when learning how to set up and run these simulations. All the errors I made when first trying to set up and run the simulation only helped me become better at the process.


I then had to run a molecular dynamics simulation (via workshop 2) to get the energy minimization and equilibration for the protein Influenza Neuraminidase 3BEQ. First time trying to run this simulation I encountered a road block, which was my own typos. Outside of the typos and making sure the input was perfect, I believe running these simulations was also not too bad. Errors also made me better at running this simulation.


Running these simulations through Putty introduced me to vim, which is a text editor. Vim allows you to edit a file in Putty. Learning Vim was not too bad also because of the Vim tutor that vim has. It teaches you the basics and everything I needed to know to successfully run the simulations.


The biggest thing I had to overcomer, for me, was to learn all these new features and remember how to use them. But once I surpassed the learning curve, It became progressively easier to get through the simulations.

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