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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 #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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- ryangmullen
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3 years 10 months ago - 3 years 10 months ago #726
by ryangmullen
Ah, if your last 6 dihedrals are intended to be improper dihedrals, then the order of the atoms is important. The central atom needs to be listed first. It looks like carbon 2 is bonded to carbons 1, 3, and 7, so dihedral 31 should have indices 2 1 3 7 rather than 7 2 1 3.
Also, the 3 parameters for the CHARMM dihedral need to be listed in the order: force_constant multiplicity angle_offset. For dihedral 31, I suspect your force_constant is 10.5 [kJ/mol], multiplicity is 4.0, and angle_offset is 180 [degrees], yes?
Also, the 3 parameters for the CHARMM dihedral need to be listed in the order: force_constant multiplicity angle_offset. For dihedral 31, I suspect your force_constant is 10.5 [kJ/mol], multiplicity is 4.0, and angle_offset is 180 [degrees], yes?
Last Edit: 3 years 10 months ago by ryangmullen.
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- aagarwa6
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3 years 10 months ago #727
by aagarwa6
Oh yes, that makes sense.
I have wrongly used the order of dihedrals as-is when converting from topology to mcf. In addition, the multiplicity listed in my mcf is supposed to be 2.0, instead 4.0 (I just found it out) - for the improper dihedrals. You are correct, the angle_offset is 180 [degrees] and force_constant is 10.5 [kJ/mol].
Let me correct all these. Thanks!
I have wrongly used the order of dihedrals as-is when converting from topology to mcf. In addition, the multiplicity listed in my mcf is supposed to be 2.0, instead 4.0 (I just found it out) - for the improper dihedrals. You are correct, the angle_offset is 180 [degrees] and force_constant is 10.5 [kJ/mol].
Let me correct all these. Thanks!
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3 years 10 months ago #729
by aagarwa6
I see what you mean, the Cassandra bond angle force constant has units of K/rad^2, whereas the ones in gromacs topology is kJ/mol/rad^2. The force constants that I used in the mcf file therefore have the wrong units of kJ/mol/rad^2. That explains a lot about why my system was not working.
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