For carrying out the simulation, we need the software: "Towhee", and a simple text editor. Please note that this software is available in LinuxOS only.
Files you need
Generating the essentials
Out of the three files, the first two have to be manually generated (towhee input and ff file) The third one is towhee executable and is to be copied from Towhee software directory Go to the software directory and locate the executable “../../towhee-7.1.0/Source/towhee”. If you have successfully installed Towhee, then you must not face any difficulty in searching for these files. We will create the input file step by step, the ff file is mostly found inbuilt. In case towhee doesn’t have your ff file, then we will edit an inbuilt file as per our need (I will cover that in a later karp).
Random simulations in an ordered way..
First, you must have a specific objective to carry forward a simulation. The objectives can vary from a complex simulation consisting of extraction of solutes using nanotubes to a simple simulation to predict physical properties of a compound (say ethanol). We will carry out a simple property calculation of Ethanol in this tutorial, and progress to better simulation as the course extends. To start with, first create a working directory in your Desktop and name it ‘Ethanol’. Copy/paste the towhee executable in “Ethanol”.
The input file
Create a blank file and name it “towhee_input” This will be our towhee configuration file or input script containing the details of the simulation In the next few slides I will guide you through each of the parameters required for a normal physical property calculation of Ethanol Our simulation will consist of equilibration and production run, first we will create input file for equilibration. For more complex simulation, different parameters will be required and the reader is requested to give the towhee manual a visit for a better understanding. For the time being, you can download this sample input script.
Input file explained
Here is an explanation of the input script. Or you can refer the manual.
The forcefield file
There are a number of ways to twitch your force field file. For now, we will be
using the inbuilt files, example the "Trappe force field" file.
This file is located in the forcefield subfolder, the "towhee_ff_TraPPE-UA" is the file we are looking for.
Further, we need to
open the page where we can get an idea about the molecule segments. Towhee provides this under the section
Now, you need to figure out which atoms are present in your system. The input script explains this part.
To run the simulation, you need to make sure all the files are in the same folder. The executable and the towhee_input files must be together, while the forcefield file location must be specified correctly in the input file. Execute the command:
./towhee > towhee_output
This will start running the towhee code and the output will be printed in the towhee_output file.
Enjoy :)Top Karpa
Let me know if I erred!!