Hi everybody. I want to simulate a super molecule in a solvent like heptane in material studio. Solvent molecules are about 700 and are around the super molecule. How can I simulate these molecules in random position and random orientation? Thank you very much in advanced.
You need to create a box using materials studio (look for the online tutorial to guide you how to do it) with the super molecule with heptane as solvent. this will generate a random orientation of the solvent around the super molecule and then you can run your simulation
There are some useful modules in material Studio, which were based on Monte Carlo Method, can do this for you. However, if you want to run MD simulation for your system. the way of how to set the initial positions of the solvent molecules around the super molecules does not matter.
You can generate random numbers by a (perl) script. For example, to generate a random number between 0 and 100 you can use
my $randomrange = 100; my $randomnumber = rand($randomrange); print $randomnumber . "\n";
As mentioned by others, you can build an empty crystal cell and then copy and paste your target molecule into it. You then use the Amorphous Cell Packing task to pack the solvent molecules around your target molecule until the density of your cell matches your target. For an example of this, please see the tutorial "Packing molecules into existing structures". Note that you can also ask questions in the official BIOVIA Materials Studio Community. https://r1132100503382-eu1-3dswym.3dexperience.3ds.com/#community:PicGX_96TjmPwe9tdYLC4w
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