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Unable to observe Insertion/Deletion in a GCMC simulation of xylene in zeolite
- aagarwa6
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3 years 10 months ago #718
by aagarwa6
Hello,
I am a PhD scholar and new to Cassandra. I was testing the applicability of the software for GCMC simulation of xylene in zeolite. However, I am unable to observe any insertion/deletion steps. The simulation setup details are as follows:
1. An OPLS/AA ff for xylene, and ClayFF for zeolite, with the xylene-zeolite cross-interactions prescribed using works by Prof. D. Theodorou in J. Phys. Chem. C 2016, 120, 21410−21426.
2. (20, 20, 20, 20, 20) % probabilities of translation, rotation, regrowth, insertion, and deletion respectively. I have tried manipulating these ratios with no luck.
3. Initial configuration generated from a zeolite-only xyz file. I tried both read_config, and add_to_config options, but the insertion event did not occur. Presently, I am only interested in getting the simulation work, therefore I tried a range of arbitrary chemical potential of mu = (50,500000) in internal units, with no luck.
4. I have tried a variety of kappa_cbmc,rotation,dihedrals with no luck.
I am attaching my input, mcf, and log file for reference. Looking for any and all assistance in the matter. I suspect my cbmc setup is flawed, especially fragmentation of the xylene molecule into a benzene ring. and atomic-methyl unit.
Thanks and regards,
Ankur Agarwal
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I am a PhD scholar and new to Cassandra. I was testing the applicability of the software for GCMC simulation of xylene in zeolite. However, I am unable to observe any insertion/deletion steps. The simulation setup details are as follows:
1. An OPLS/AA ff for xylene, and ClayFF for zeolite, with the xylene-zeolite cross-interactions prescribed using works by Prof. D. Theodorou in J. Phys. Chem. C 2016, 120, 21410−21426.
2. (20, 20, 20, 20, 20) % probabilities of translation, rotation, regrowth, insertion, and deletion respectively. I have tried manipulating these ratios with no luck.
3. Initial configuration generated from a zeolite-only xyz file. I tried both read_config, and add_to_config options, but the insertion event did not occur. Presently, I am only interested in getting the simulation work, therefore I tried a range of arbitrary chemical potential of mu = (50,500000) in internal units, with no luck.
4. I have tried a variety of kappa_cbmc,rotation,dihedrals with no luck.
I am attaching my input, mcf, and log file for reference. Looking for any and all assistance in the matter. I suspect my cbmc setup is flawed, especially fragmentation of the xylene molecule into a benzene ring. and atomic-methyl unit.
Thanks and regards,
Ankur Agarwal
This email address is being protected from spambots. You need JavaScript enabled to view it.
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- ryangmullen
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3 years 10 months ago #722
by ryangmullen
Hi Ankur,
Looking over your files there are a few issues:
(1) The toluene mcf only identifies one 12-atom fragment. There should be a second 5-atom fragment consisting of the central carbon atom of the methyl group, the 3 hydrogen atoms in the methyl group, and the aromatic carbon to which the methyl carbon is bonded. It appears that you edited the mcf by hand, in order to input both OPLS and CHARMM dihedrals. Did you also edit the fragment info, or did mcfgen.py mistakenly identify only a single fragment?
(2) The temperature in your input file is 623.15. - note the period at the end of the value. As a result, the log file shows that the temperature is ******* K (likely an undefined value). Remove that second period and Cassandra will read your temperature correctly.
There are a few minor issues too:
(3) It appears that you only have 4 sets of LJ parameters in your toluene model, but that you've listed each atom as a different type. You custom mixing rule section could be simplified greatly if you only used 2 carbon atom types and 2 hydrogen atom types.
(4) Lastly, your chemical potential values are very large and positive. They likely correspond to a very compressed liquid phase. Generally speaking, chemical potentials in the gas phase or liquid phase at standard pressure are negative.
Looking over your files there are a few issues:
(1) The toluene mcf only identifies one 12-atom fragment. There should be a second 5-atom fragment consisting of the central carbon atom of the methyl group, the 3 hydrogen atoms in the methyl group, and the aromatic carbon to which the methyl carbon is bonded. It appears that you edited the mcf by hand, in order to input both OPLS and CHARMM dihedrals. Did you also edit the fragment info, or did mcfgen.py mistakenly identify only a single fragment?
(2) The temperature in your input file is 623.15. - note the period at the end of the value. As a result, the log file shows that the temperature is ******* K (likely an undefined value). Remove that second period and Cassandra will read your temperature correctly.
There are a few minor issues too:
(3) It appears that you only have 4 sets of LJ parameters in your toluene model, but that you've listed each atom as a different type. You custom mixing rule section could be simplified greatly if you only used 2 carbon atom types and 2 hydrogen atom types.
(4) Lastly, your chemical potential values are very large and positive. They likely correspond to a very compressed liquid phase. Generally speaking, chemical potentials in the gas phase or liquid phase at standard pressure are negative.
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3 years 10 months ago #723
by aagarwa6
Hi Ryan,
Thank you so much for the swift reply!
You are correct, I have generated the mcf file myself, specifying the dihedrals listed in the molecule's atomistic topology file. I also added the fragment information myself by declaring the ring atoms into a single fragment, following the tutorials.
- From your suggestion, I will add the rest of the methyl atoms connected to the ring into the second fragment.
That's a great suggestion on simplification of the LJ parameters of the atoms of the toluene. I will make that change to streamline the potential parameter file, which would make it more readable.
You are correct, my choice of chemical potential reported in the files shared is wrong for the system I intended to test, and is just a consequence of me manipulating values to see if something works. My apologies for the confusion.
Thanks for helping me out in using this. Let me implement all these into my system.
Thanks!
Ankur
Thank you so much for the swift reply!
You are correct, I have generated the mcf file myself, specifying the dihedrals listed in the molecule's atomistic topology file. I also added the fragment information myself by declaring the ring atoms into a single fragment, following the tutorials.
- From your suggestion, I will add the rest of the methyl atoms connected to the ring into the second fragment.
That's a great suggestion on simplification of the LJ parameters of the atoms of the toluene. I will make that change to streamline the potential parameter file, which would make it more readable.
You are correct, my choice of chemical potential reported in the files shared is wrong for the system I intended to test, and is just a consequence of me manipulating values to see if something works. My apologies for the confusion.
Thanks for helping me out in using this. Let me implement all these into my system.
Thanks!
Ankur
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- ryangmullen
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3 years 10 months ago - 3 years 10 months ago #724
by ryangmullen
Hi Ankur,
I looked over Toluene.mcf. Your 36 dihedrals fall into 3 categories:
( A ) 1-24 are OPLS style, but only coefficient a2 is non-zero.
( B ) 25-30 are OPLS style, but all coefficients are zero.
( C ) 31-36 are CHARMM style, but are not applied to 4 consecutively bonded atoms. Are you sure these are correct?
Dihedrals of Type A (and B ) can be converted to CHARMM-style dihedrals, in which case you can use the script mcfgen.py to generate your mcf. mcfgen.py will map the dihedral parameters to the correct atoms and identify the right set of fragments.
Ryan
I looked over Toluene.mcf. Your 36 dihedrals fall into 3 categories:
( A ) 1-24 are OPLS style, but only coefficient a2 is non-zero.
( B ) 25-30 are OPLS style, but all coefficients are zero.
( C ) 31-36 are CHARMM style, but are not applied to 4 consecutively bonded atoms. Are you sure these are correct?
Dihedrals of Type A (and B ) can be converted to CHARMM-style dihedrals, in which case you can use the script mcfgen.py to generate your mcf. mcfgen.py will map the dihedral parameters to the correct atoms and identify the right set of fragments.
Ryan
Last Edit: 3 years 10 months ago by ryangmullen.
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