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farzinfarzin 

Why dosn't the cell length change under pressure?

Hi all,

I simulated a periodic box including a graphene sheet at the middle (Fig. is attached). I did some NPT dynamics under the atmosphere pressure, but the length of the box didn't reduced in C direction (normal to graphene). This also happens when some polymer chains are packed into the empty space of the box with low density (e.g. 0.5 g/cm3). What is the reason?


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Thank you in advance.
Farzin
Best Answer chosen by farzin
CarstenCarsten (Accelrys) 
Please use Souza-Martin or Parrinello as barostat.

Your system is quite anisotropic and Anderson and Berendsen barostats are not a good choice then.

From the help for Berendsen:
As implemented, this method changes the cell uniformly, so that the size of the cell is changed, but not its shape. Therefore, it is inappropriate for simulations such as crystal phase transitions, where both the cell size and shape are expected to change.

And for Andersen:
However, this method is not very useful for studying materials under anisotropic stress or undergoing phase transitions, which involve changes in both cell lengths and cell angles

All Answers

CarstenCarsten (Accelrys) 
Please use Souza-Martin or Parrinello as barostat.

Your system is quite anisotropic and Anderson and Berendsen barostats are not a good choice then.

From the help for Berendsen:
As implemented, this method changes the cell uniformly, so that the size of the cell is changed, but not its shape. Therefore, it is inappropriate for simulations such as crystal phase transitions, where both the cell size and shape are expected to change.

And for Andersen:
However, this method is not very useful for studying materials under anisotropic stress or undergoing phase transitions, which involve changes in both cell lengths and cell angles
This was selected as the best answer
farzinfarzin
Dear Carsten,
Thank you for your helpful answer.

Farzin
farzinfarzin
Dear Carsten,

Thank you again for you help. Following your instructions, I created a periodic box including a graphene sheet at the middle sounded by polymer chains (Fig. is attached). Then I performed NPT dynamics under the atmosphere pressure with Souza-Martins and Parrinello barostats, in order to reach real density. However, the angles of the box were changed in addition to the lengths, although I had constrained the angles. Is there any way I can fix the angles during NPT and keep the cell walls orthogonal?

User-added image

Thank you
Farzin