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1
General / Re: Mg and K cations .def file
« Last post by David Dubbeldam on May 26, 2020, 04:57:06 PM »
All structure, molecule and force field files are examples. For you own use case, you need to construct these files with the exact parameters that you want.
2
Input files and parameters / pseudo_atom radii
« Last post by rshukre on May 18, 2020, 03:50:02 AM »
Dear all,

The pseudo_atom radii for N_N2 and NCOM_N2  are 0.7 in the pseudo_atoms.def file. The model for N2 molecule is taken from Potoff and Siepmann as the charge values for N and NCOM match with the partial charges given to these sites of N2 molecule of Potoff and Siepmann. How is the pseudo atom radius of 0.7 defined? What is the basis for the same. The experimental bond length of N2 molecule is 1.1 A.
The reason I am asking this question is because I want to define the pseudo_atoms for two CO models developed by Calero et al  (2012) and Piper et al (1984). For these models, I have the LJ parameters, charges and the distance of the sites from the COM of the molecule. What should be the basis to define the pseudo_atom radii for each site of these models?

Thanks,
Rajasi
3
General / Mg and K cations .def file
« Last post by ergrhn on May 17, 2020, 09:20:06 PM »
Hello everyone,

I am trying to calculate H2 adsorption in clinoptilolite. I want to use Mg and K as cations.

But there are not any .def file belong these atoms.

How can i solve this problem.


4
Negative excess adsorption indicates that you are in the liquid phase. That happens when you go above the vapor pressure.
5
Input files and parameters / Re: MC and MD inconsistency
« Last post by David Dubbeldam on May 14, 2020, 07:07:21 PM »
A common inconstancy between MC and MD is the VDW potential. Make sure you use a shifted VDW potential for MC.
6
Depending on the value of 'f' you could probably rewrite that functional form into into another form that is supported (using cosine and sine rules). If that is not possible, another option is add the functional form in the code.
7
Input files and parameters / Re: Gibbs Ensemble MC
« Last post by Christopher on May 06, 2020, 08:48:07 PM »
Hello and thanks a bunch for your help!

It's really usefull and saves me a lot of extra time! Great!
8
Input files and parameters / Torsional potential with phase angle term
« Last post by aemelianova on May 01, 2020, 03:43:09 AM »
Dear Prof. Dubbeldam,

I am trying to implement the force field with the torsion potential for a molecule which includes a non-zero phase angle term f to account for asymmetric rotational barriers:
U = C_0 + C1[1 + cos(phi +f) ] + C2[1-cos(2(phi + f)] + C3[1-cos(3(phi + f)]
and could not find the proper form in the manual.
Is there a way to implement this form of the potential in RASPA?

Thank you!

9
Input files and parameters / MC and MD inconsistency
« Last post by skvara.jiri on April 28, 2020, 05:57:02 PM »
Dear RASPA users,
I tried to compare MD and MC runs in NPT ensemble for 2-methylbutane molecules which forcefield is attached to Raspa as an example. I did not modify the force field but I am not able to reach the same density in MC and MD (in MD the density is lower by 100 kg/m^3). I tried simulations at different state point and I was not able to match MC and MD Raspa results. I also tried simulations of different molecules and my results match only for water all other molecules differed in density.

I had found that MD results are changes when I am using the option "ComputeMolecularPressure yes". I can't see why there should be any change in density with this option if the barostat is working properly. If this option is necessary for barostat, then the NPT run should not be performed without this command.


Attached you can find my MD simulation script (system did not allow me to attach the file itself). I will be glad for your advice. I believed that problem is in my simulation settings.

SimulationType                   MolecularDynamics
NumberOfCycles         50000000
NumberOfInitializationCycles   1000
NumberOfEquilibrationCycles   10000
PrintEvery                       100
RestartFile                      no

InitEnsemble    NVT
RunEnsemble   NPT
TimeStep   0.001

Forcefield                       local
CutOff                           12
ChargeMethod               Ewald
CutOffVDW         12
CutOffCoulomb         12

Box 0
BoxLengths 37 37 37
ExternalTemperature 293.15
ComputeMolecularPressure yes
ExternalPressure 101325

Movies yes
WriteMoviesEvery 1000


Component 0 MoleculeName             2-methylbutane
            MoleculeDefinition       local
       ReinsertionProbability   1.0
       TranslationProbability   1.0
            CreateNumberOfMolecules  256
      
10
Dear Dubbeldam,

I'm using RASPA to simulate the alkane adsorption in Montmorillonite. But in the output , the absolute adsorption is zero, the excess loading is negative, I don't know why and how to get the correct amount of adsorption.

Kind regards,
Yadi Jiang

*************
This is the component's critical parameter´╝Ü792K, 0.98MPa, 0.8.
(In the simulation, temperature is 358K, pressure is 30MPa,40MPa.)

*************
This is the simulation.input file:

SimulationType                MonteCarlo
NumberOfCycles                100000
NumberOfInitializationCycles  50000
PrintEvery                    1000
RestartFile                   no

ContinueAfterCrash no
WriteBinaryRestartFileEvery 5000

ChargeMethod                    Ewald
Forcefield                      clayff  //Custom force field
CutOffVDW                       12.5
RemoveAtomNumberCodeFromLabel   no

Framework 0
FrameworkName 10-MMT
UseChargesFromCIFFile no
UnitCells 3 3 3
HeliumVoidFraction  1
ExternalTemperature 358
ExternalPressure 3e7 4e7
Movies yes
WriteMoviesEvery  5000
ComputeDensityProfile3DVTKGrid           yes
WriteDensityProfile3DVTKGridEvery        1000
DensityProfile3DVTKGridPoints            150 150 150
AverageDensityOverUniteCellsVTK          yes
DensityAverageTypeVTK                    FullBox

Component 0 MoleculeName              C22
            MoleculeDefinition        TraPPE
            TranslationProbability    1.0
            RotationProbability       1.0
            ReinsertionProbability    1.0
            IdentityChangeProbability 0.0
            SwapProbability           1.0
            CreateNumberOfMolecules   0


***************
The force field parameter:

# general rule for shifted vs truncated
shifted
# general rule tailcorrections
no
# number of defined interactions
4
# type interaction, parameters.    IMPORTANT: define shortest matches first, so that more specific ones overwrites these
O_             lennard-jones    78.263        3.5532
Al_            lennard-Jones    0.00067       4.7943
Si_            lennard-Jones    0.000926      3.7064
Ca_            lennard-Jones    50.362        3.2237

# general mixing rule for Lennard-Jones
Lorentz-Berthelot

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