Author Topic: NPT-Flexible framework  (Read 41 times)

isaaraujo

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NPT-Flexible framework
« on: November 11, 2021, 08:37:01 AM »
Hello,
I am performing MD in the NPT ensemble. The system is an illite slit pore filled with water and an electrolyte. I am considering the framework flexible (the only bond considered in the framework is between hydrogen and oxygen). When I run NPT simulations the structure moves out of the simulation box and looks pretty deformed.
If I consider the framework to be rigid in the NPT ensemble the simulation crashes even at very small time steps and the output file for the framework (.cif) shows NAN values.
What could be a reason for that, and is there any way to address this problem in RASPA? Is there a way to restrain all hydrogen bonds in the framework?

#CoreShells bond  BondDipoles UreyBradley bend  inv  tors improper-torsion bond/bond bond/bend bend/bend stretch/torsion bend/torsion
          0    1            0           0    0    0     0                0         0         0         0               0            0
#bond stretch atom n1-n2, equilibrium distance, bondforce-constant
OH  HO  HARMONIC_BOND     557706.438693      1.00       
Thank you

AHF

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Re: NPT-Flexible framework
« Reply #1 on: November 26, 2021, 06:50:40 PM »
You are running a simulation in NPT ensemble which means the volume of your simulation box is no longer constant. The unit cell can change in shape and size. Please check dimensions of your unit cell (a, b, c, alpha, beta, gamma) at every step, this way you can confirm how volume is changing.

Hope it helps.
Cheers,

isaaraujo

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Re: NPT-Flexible framework
« Reply #2 on: December 01, 2021, 04:29:31 PM »
Thank you very much for your response!
Do you know if it is possible to run NPT simulations with a rigid framework? When I run the NPT simulations keeping framework rigid, I see that I have two simulation boxes: One for the framework(which is a slit pore) and one for the the adsorbate(water molecules). Only the simulation cell of the water molecules change volume, the simulation cell of the adsorbent is kept fixed, therefore when there is change in volume in the water molecules simulation cell, the framework and molecules get very close and the simulation crashes. Is there a way to keep framework rigid but allow change in the framework simulation box?
Thank you