Compounds with a linear group (N≡C– or HC≡C–) attached to a 5-membered ring cause simulations to crash (tested with Gromacs). Before the crash, the rings become distorted. Compounds with a 6-membered ring are unaffected. By comparing the parameters generated for compounds with 5- and 6-membered rings, the issue seems to be with the coefficients of proper dihedrals that terminate with the nitrogen or carbon. In the case of 5-membered rings, the coefficients are non-zero. In some compounds, the torsion angle that terminates in the N≡C– carbon also has different coefficients than those in compounds with 6-membered rings. Making modifications to these parameters seems to fix the issue. The problem can be reproduced with the following compounds:
Compounds with a linear group (N≡C– or HC≡C–) attached to a 5-membered ring cause simulations to crash (tested with Gromacs). Before the crash, the rings become distorted. Compounds with a 6-membered ring are unaffected. By comparing the parameters generated for compounds with 5- and 6-membered rings, the issue seems to be with the coefficients of proper dihedrals that terminate with the nitrogen or carbon. In the case of 5-membered rings, the coefficients are non-zero. In some compounds, the torsion angle that terminates in the N≡C– carbon also has different coefficients than those in compounds with 6-membered rings. Making modifications to these parameters seems to fix the issue. The problem can be reproduced with the following compounds:
Mol_01: o1cc(C#C)cc1 [ dihedrals ] ; PROPER DIHEDRAL ANGLES ; ai aj ak al funct c0 c1 c2 c3 c4 c5 7 6 3 4 3 9.079 0.000 -9.079 -0.000 -0.000 0.000 6 3 4 5 3 9.079 0.000 -9.079 -0.000 -0.000 0.000
Mol_02: o1cc(C#N)cc1 7 6 3 4 3 9.079 0.000 -9.079 -0.000 -0.000 0.000 6 3 4 5 3 9.079 0.000 -9.079 -0.000 -0.000 0.000
Mol_03: o1c2ccccc2c(C#N)c1 11 8 9 10 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
Mol_04: o1cccc1C#Cc2ccccc2 7 6 5 1 3 9.079 0.000 -9.079 -0.000 -0.000 0.000