1
General / Re: list of configurational moves in .def file
« on: June 23, 2022, 06:17:44 PM »
Got it! Thank you so much for your time and clear explanation
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2
General / list of configurational moves in .def file
« on: June 21, 2022, 08:40:19 PM »
Dear Prof. Dubbeldam and RASPA community,
I am simulating adsorption in MOFs of an adsorbate with large molecules which shows zero adsorption in UiO-66 (although it is quite significant in other MOFs of similar pore size). I nevertheless suspect it is due to insertion issues.
I am therefore trying to run configurational-bias Monte Carlo, which is, in my understanding, requires a list of configurational moves in .def file, for example, as it is listed in dimethylpropane.def file:
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
433.75
3196300.0
0.197
# number of atoms
5
# atomic types
0 CH3_sp3
1 C_sp3
2 CH3_sp3
3 CH3_sp3
4 CH3_sp3
...
...
...
# Number of config moves
4
# nr fixed, list
2 0 1
2 1 4
2 1 2
2 1 3
Could you please give me some details on how this list is constructed?
I am simulating adsorption in MOFs of an adsorbate with large molecules which shows zero adsorption in UiO-66 (although it is quite significant in other MOFs of similar pore size). I nevertheless suspect it is due to insertion issues.
I am therefore trying to run configurational-bias Monte Carlo, which is, in my understanding, requires a list of configurational moves in .def file, for example, as it is listed in dimethylpropane.def file:
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
433.75
3196300.0
0.197
# number of atoms
5
# atomic types
0 CH3_sp3
1 C_sp3
2 CH3_sp3
3 CH3_sp3
4 CH3_sp3
...
...
...
# Number of config moves
4
# nr fixed, list
2 0 1
2 1 4
2 1 2
2 1 3
Could you please give me some details on how this list is constructed?
3
Input files and parameters / Re: Zero adsorption when intra vdW and Coulomb are on
« on: January 11, 2021, 09:30:24 PM »
Dear Prof. Dubbeldam,
Thank you very much for your reply.
I computed and specified the IdealGasRosenbluthWeight but it did not give any improvement. I also noticed that, when intra vdW is on and intra Coulomb is off, adsorption is not zero, but still much lower (and close to zero) than the case with internal non-bonded interactions turned off (and much lower than what is given here http://aam.ceb.cam.ac.uk/mof-explorer/CWACapture/).
For example, for IRMOF-6, I was only able to get adsorption close to what is given in the data base with turned off internal non-bonded interactions.
Interestingly, it happens for all the MOFs from RASPA library (I used GenericMOFs force field for all of them) and does not happen for any of the zeolites.
Thank you very much for your reply.
I computed and specified the IdealGasRosenbluthWeight but it did not give any improvement. I also noticed that, when intra vdW is on and intra Coulomb is off, adsorption is not zero, but still much lower (and close to zero) than the case with internal non-bonded interactions turned off (and much lower than what is given here http://aam.ceb.cam.ac.uk/mof-explorer/CWACapture/).
For example, for IRMOF-6, I was only able to get adsorption close to what is given in the data base with turned off internal non-bonded interactions.
Interestingly, it happens for all the MOFs from RASPA library (I used GenericMOFs force field for all of them) and does not happen for any of the zeolites.
4
Input files and parameters / Zero adsorption when intra vdW and Coulomb are on
« on: December 10, 2020, 07:12:27 PM »
Dear Prof. Dubbeldam and RASPA community,
I am trying to reproduce adsorption of sarin on IRMOF-6 (http://aam.ceb.cam.ac.uk/mof-explorer/CWACapture/).
I use GCMC ensemble and the molecule is flexible. The MOF charges are taken from CoRE MOF DDEC database.
I was able to get a reasonable value for adsorption when intra vdW and Coulomb interactions are turned off.
However, I believe it should be taken into account for a correct model. When I turn it on (same case for 1-4 and 1-5 or only 1-5 neighbors), the resulted adsorption is zero.
I did the following to make sure only this factor gives such a result:
- I tested the model of the molecule with bulk NPT (with intra interactions) and the result was reasonable and there was nothing strange with the system
- On the same model of IRMOF-6 I exactly reproduced adsorption of CO2 from literature
- Sarin with intra vdW and Coulomb did not give a zero adsorption on a zeolite (NaX)
Do you know what might cause the problem and is there a way to resolve it?
Thank you very much,
Alina
I am trying to reproduce adsorption of sarin on IRMOF-6 (http://aam.ceb.cam.ac.uk/mof-explorer/CWACapture/).
I use GCMC ensemble and the molecule is flexible. The MOF charges are taken from CoRE MOF DDEC database.
I was able to get a reasonable value for adsorption when intra vdW and Coulomb interactions are turned off.
However, I believe it should be taken into account for a correct model. When I turn it on (same case for 1-4 and 1-5 or only 1-5 neighbors), the resulted adsorption is zero.
I did the following to make sure only this factor gives such a result:
- I tested the model of the molecule with bulk NPT (with intra interactions) and the result was reasonable and there was nothing strange with the system
- On the same model of IRMOF-6 I exactly reproduced adsorption of CO2 from literature
- Sarin with intra vdW and Coulomb did not give a zero adsorption on a zeolite (NaX)
Do you know what might cause the problem and is there a way to resolve it?
Thank you very much,
Alina
5
Input files and parameters / Density by NPT MC and MD
« on: August 03, 2020, 12:35:07 AM »
Dear Prof. Dubbeldam and RASPA users,
I was trying to calculate the density of the bulk liquid using NPT ensemble with MC and validate by NPT MD simulation.
I am using the same force field and the rest of the parameters for the molecule. I got the expected result (close to the experimental value) with MC which also agrees well with MD simulation in LAMMPS. However, MD result by RASPA is much higher (about 60 kg/m3 difference). Both results were well equilibrated.
I was trying to turn on/off tail correction and change the time step, and it did not change the result significantly.
What may be the reason of this discrepancy?
I was trying to calculate the density of the bulk liquid using NPT ensemble with MC and validate by NPT MD simulation.
I am using the same force field and the rest of the parameters for the molecule. I got the expected result (close to the experimental value) with MC which also agrees well with MD simulation in LAMMPS. However, MD result by RASPA is much higher (about 60 kg/m3 difference). Both results were well equilibrated.
I was trying to turn on/off tail correction and change the time step, and it did not change the result significantly.
What may be the reason of this discrepancy?
6
Input files and parameters / Torsional potential with phase angle term
« on: May 01, 2020, 04:43:09 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!
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!
7
Input files and parameters / Average configuration as restart-file
« on: August 22, 2019, 10:19:27 PM »
Hello Prof. Dubbeldam,
Is there a way to have a restart-file at the end of a simulation with average configurations? Or alternatively is there a way to save configurations each several cycles/steps as restart-files while the simulation is progressing?
Thanks,
Alina
Is there a way to have a restart-file at the end of a simulation with average configurations? Or alternatively is there a way to save configurations each several cycles/steps as restart-files while the simulation is progressing?
Thanks,
Alina
8
Simulation algorithms and theory / Re: GCMC combination with NpT-MD
« on: March 26, 2019, 03:22:00 PM »
Thank you very much for the answer.
9
Simulation algorithms and theory / GCMC combination with NpT-MD
« on: March 15, 2019, 08:52:50 PM »
Dear Prof. Dubbeldam,
RASPA documentation shows how to perform hybrid MD/MC simulation by a combination GCMC with short NVE MD-run.
Is there any way to set up a combination of GCMC and short MD-run in NpT ensemble (instead of NVT) in RASPA?
Thank you,
Alina
RASPA documentation shows how to perform hybrid MD/MC simulation by a combination GCMC with short NVE MD-run.
Is there any way to set up a combination of GCMC and short MD-run in NpT ensemble (instead of NVT) in RASPA?
Thank you,
Alina
10
Input files and parameters / Re: chemical potential in input file
« on: October 01, 2018, 08:06:52 PM »
Prof. Dubbeldam,
Thank you very much for the answer.
Thank you very much for the answer.
11
Input files and parameters / chemical potential in input file
« on: October 01, 2018, 05:22:34 PM »
Hello!
I have a few questions:
- is there any way to set up chemical potential in an input file instead of pressure?
- can I somehow set up some other EOS instead of Peng-Robinson?
Thank you.
I have a few questions:
- is there any way to set up chemical potential in an input file instead of pressure?
- can I somehow set up some other EOS instead of Peng-Robinson?
Thank you.
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