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Unable to observe Insertion/Deletion in a GCMC simulation of xylene in zeolite
- aagarwa6
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- ryangmullen
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3 years 11 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 11 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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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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3 years 10 months ago #725
by aagarwa6
Thanks Ryan!
I generated the dihedrals in mcf file from the LigParGen web server for OPLS/AA atomic force field. I ended up using a mix of CHARMM and OPLS in mcf file because the atomistic file contained dihedrals of two types (in gromacs terms): mcf file "OPLS" = Ryckaert-Bellemans dihedral type3, and mcf file "CHARMM" = periodic improper dihedral type4.
Let me check the dihedrals more closely and incorporate conversion between dihedrals and test simulation. Thanks again for your valuable input!
Ankur
I generated the dihedrals in mcf file from the LigParGen web server for OPLS/AA atomic force field. I ended up using a mix of CHARMM and OPLS in mcf file because the atomistic file contained dihedrals of two types (in gromacs terms): mcf file "OPLS" = Ryckaert-Bellemans dihedral type3, and mcf file "CHARMM" = periodic improper dihedral type4.
Let me check the dihedrals more closely and incorporate conversion between dihedrals and test simulation. Thanks again for your valuable input!
Ankur
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