Author Topic: Problem with MD in NPT ensemble  (Read 70 times)

isaaraujo

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Problem with MD in NPT ensemble
« on: September 09, 2021, 03:02:36 AM »
Dear RASPA users,

I am performing a MD simulation in the NPT ensemble. My system is composed of a flexible illite slit pore with water molecules and an electrolyte. When I visualize my simulation, I observe a deformation in the illite structure and that the illite structure is no longer restricted to the simulation box. Is it possible to run MD in NPT simulations using a rigid framework? I also would like to know if it is possible to immobilize the center of mass of the illite layers to avoid such problem.

Thank you!
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Some of the simulation inputs:
#CoreShells bond  BondDipoles UreyBradley bend  inv  tors improper-torsion bond/bond bond/bend bend/bend stretch/torsion bend/torsion
          0    2            0           0    4    0     0                0         0         0         0               0            0
#bond stretch atom n1-n2, equilibrium distance, bondforce-constant
OH  HO  HARMONIC_BOND     278853.270000    1.00
OS  HO  HARMONIC_BOND     278853.270000    1.00
#bond bending atom n1-n2-n3, equilibrium angle, bondforce-constant
Si OH HO HARMONIC_BEND    15097.4537000    109.47000
Si OS HO HARMONIC_BEND    15097.4537000    109.47000
Al OH HO HARMONIC_BEND    15097.4537000    109.47000
Al OS HO HARMONIC_BEND    15097.4537000    109.47000
_________________________________________________________________________

SimulationType                   MolecularDynamics
NumberOfCycles                         80000
NumberOfEquilibrationCycles      80000
RestartFile                      no

Ensemble          NPT

Forcefield                       CLAYFF
RemoveAtomNumberCodeFromLabel yes

Framework 0
FrameworkName illite
UnitCells       1 1 1
ExternalTemperature 330.0
ExternalPressure  10e6
ComputeMolecularPressure yes

FrameworkDefinitions CLAYFFLEXIBLE
FlexibleFramework yes

Movies yes
WriteMoviesEvery 1000

Component 0 MoleculeName                 kalium
       MoleculeDefinition           Cations
       TranslationProbability       1.0
       RandomTranslationProbability 1.0
       ExtraFrameworkMolecule       yes
       CreateNumberOfMolecules      30

Component 1 MoleculeName                   water
       StartingBead         0
            MoleculeDefinition             Clayff
            TranslationProbability         1.0
            RotationProbability            1.0
            ReinsertionProbability         1.0
            CreateNumberOfMolecules        280

Component 2 MoleculeName                   Cl
       StartingBead         0
            MoleculeDefinition             Clayff
       RandomTranslationProbability   1.0
            RotationProbability            1.0
            CreateNumberOfMolecules        4

Component 3 MoleculeName                   Na
       StartingBead         0
            MoleculeDefinition             Clayff
        RandomTranslationProbability   1.0
            RotationProbability            1.0
            CreateNumberOfMolecules        4