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khemistkevinkhemistkevin 

What density to use in amorphous cell

I'm very new to Materials Studio and am attempting to get estimates of miscibility for binary mixtures. I've completed the 'calculating the miscibility of 2 polymers' tutorial, but it's not clear how the density should be set when creating the amorphous cell. Is the density used to construct the amorphous cell based on experiments? Is there an acceptable way to estimate the density?

If it helps, I'm trying to run a calculation on a drug molecule and a shorter chain representation of a polymer. 

Thanks!
Best Answer chosen by khemistkevin
Jason DeJoannisJason DeJoannis
Hi khemistkevin,
 
In the tutorial, a density of 0.9 g/cc was used. That is somewhat arbitrary, but is in the right ballpark as the density of polystyrene is in the range 0.96-1.04 and polypropylene is in the range 0.895-0.92. For liquids, it is sufficient to relax the density of the system using an NPT dynamics run. For polymers, it is recommended to subject the system to annealing as well, as illustrated in the “Calculating the diffusivity of a gas in a polymer” tutorial (and the Meunier reference).
 
If the density is unknown, it is usually reasonable to start from the default 1.0 and equilibrate with NPT. Another way to estimate density, if you cannot find it online or in a handbook, is using the Synthia module.
 
Best,
Jason
 

All Answers

Jason DeJoannisJason DeJoannis
Hi khemistkevin,
 
In the tutorial, a density of 0.9 g/cc was used. That is somewhat arbitrary, but is in the right ballpark as the density of polystyrene is in the range 0.96-1.04 and polypropylene is in the range 0.895-0.92. For liquids, it is sufficient to relax the density of the system using an NPT dynamics run. For polymers, it is recommended to subject the system to annealing as well, as illustrated in the “Calculating the diffusivity of a gas in a polymer” tutorial (and the Meunier reference).
 
If the density is unknown, it is usually reasonable to start from the default 1.0 and equilibrate with NPT. Another way to estimate density, if you cannot find it online or in a handbook, is using the Synthia module.
 
Best,
Jason
 
This was selected as the best answer
said2018said2018
hi jason, 
i need your help in MS simulation can you help?