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Packing a system!

In this page, you will be instructed on how to build a system for your Molecular dynamics or Monte Carlo simulation, or any other simulation thereof, using an open source tool: Packmol.

Packmol Files

Getting Started

Computational simulations are performed on a system.
What do I mean by a system?
Just a simple pdb file that has the required number of molecules of the compounds or elements you wish to work on.


Remember: Packmol works with mol2 and xyz format files too.
Changes: You need to change ".pdb" to ".xyz" or ".mol2", as per the need!

The quick three steps

  • Get the pdb/xyz/mol2 files for each component of your system.
  • Get a suitable packmol script.
  • Run the script using the command:
    ./packmol < mixture.txt

The Proper Elucidation

Equipments required:
1) Crystal Pdb file for each of the compounds/elements.
2) Packmol software. It is an open source software:
   PS: Don't forget to register. ;)

That's all you need.
I will assume that you followed the installation process on their website and did the needful.
If you face any installation problems you can direct those mails to their owners.

1. Pdb

We need the pdb files containing the coordinates of a single molecule of our compound.
If it is a complex that you are working on, then you need the pdb of the complex.
But make sure it has the coordinates of only one such complex.

How to get the pdb file:

  • a. Geometry optimization using Quantum Calculations
  • b. Get it from pdb databank. (Recommended method)
  • c. From other source (as per your need)

2. Script

To run packmol, you need a .txt file that will specify the quantity of different molecules and constraint that you want to apply to get a desired system.
Packmol gives it's user the ability to specify the size of the system and the number of molecules of each compound in the system.
Apart from these, you can also specify whether you want Packmol to randomly distribute the molecules inside the box or to place it exactly at a fixed coordinate. There are some other options too (manual).

Here is a nicely commented Packmol script file to help you out.
Save this file as mixture.txt, and read it through to get a feel.
Feel free to refer to the manual for more help.

3. Run

If you have come this far, then we are almost done!!
Open cmd or terminal, crawl to the present directory and type:

Linux: ./packmol < mixture.txt
CMD: packmol.exe < mixture.txt

The code should run (without error) and an output file will be created.
You can visualize the output in VMD or any other visualizing tool of your choice.

Danke!! :)

Top Karpa

Let me know if I erred!!