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Topics - isaaraujo

General / Energy Drift - Cations
January 08, 2022, 09:52:04 AM
Dear Dr. Dubbeldam,

I am simulating adsorption of water and salt on a clay slit pore using MD simulations. First I minimized the clay structure + cations in the NPT ensemble using the Baker minimization method. Subsequently I equilibrated the structure in the NPT ensemble. However I notice that during the equilibration, the energy drifts increase gradually at each step. For structures that do not have cations as extra framework, I don't observe this issue. Is there a way to address this problem in RASPA?
I have another question regarding energy drifts in the simulation. For another system that I am simulating and that does not contain any cations I can reach an energy drift around 1x10^-5 during equilibration. However, when production steps start, the energy drift started gradually increasing. What could be a reason for that? 

SimulationType                   MolecularDynamics
NumberOfCycles                         20000
NumberOfInitializationCycles     20000
NumberOfEquilibrationCycles      500000
RestartFile                      yes
PrintEvery      10000
ContinueAfterCrash            no
WriteBinaryRestartFileEvery   2000
Ensemble          NPT

CutOff                           9.0
Movies yes
WriteMoviesEvery 20000
PrintEvery       25000
PrintPropertiesEvery 25000

TimeStep          0.0005
Forcefield                       CLAYFF
RemoveAtomNumberCodeFromLabel yes

Framework 0
FrameworkName superillite_complete20
UnitCells       1 1 1
ExternalTemperature 330.0
ComputeMolecularPressure yes

FlexibleFramework yes
FrameworkDefinitions CLAYFFLEXIBLE
ExternalPressure 5000000.0

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

Thank you

General / NPT Simulations
December 01, 2021, 05:25:16 PM
Dear Dr. Dubbeldam,

Is it possible to run NPT simulations in a rigid framework ( in my case it is a clay slit pore)? 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 (specially in the z direction)?

Thank you
General / NPT-Flexible framework
November 11, 2021, 08:37:01 AM
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