Creating the System
Packing the system
Packmol
Molecular simulations are sort of "modelling the reality" technique. How many molecules does a 60 gm of ethanol have? A whopping avogadro number of molecules.
But our computers can hardly handle even a millionth of that number. In ms studies, people generally study upto million atoms (in extraordinary cases)
and in our simulation we are going to take 500 molecules. If you are thinking if that is a good enough number of molecules to model reality, well,
it is up to you to find out. Why not perform the calculations and watch out yourself?
We have the pdb file for our single ethanol molecule. Next we need to generate a system of many such ethanol molecules.
To do so, we will use the open source software, developed by Dr. Martinez, 'Packmol'.
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Create a folder and copy paste the packmol executable from the packmol directory
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Copy paste the pdb file generated from vmd (new.pdb)
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We need a packmol script to specify our system, this one should help
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Save the above script as "mixture.txt". You can follow this tutorial to get more insights on creating this file.
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Open command prompt from the current directory, and execute the packmol script: packmol.exe < mixture.txt
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A file named final.pdb will be created
As always, again it is lethal to carry out work you don't understand. The above tutorial mentioned explains in a sweet way the packmol script.
Do give a look. In our script, I have specified 500 ethanol molecules and all these molecules are clustered in a box of dimensions 50X50X100.
Why? Well, you can begin with any larger box, but the larger the box the more time it will take to equilibrate (why?), and if you take a smaller box,
packmol might find it difficult to pack the system (too cramped?).
Let's have a look at what we have created up till now.
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Open vmd. Go to File -> New Molecule.. -> Browse. -> locate and select the final.psf file. Click Load.
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Again select Browse -> Locate and select the final.pdb file. Click Load.
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The VMD Display window will show your system, something like the pic shown below
500 Ethanol molecules
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