Hello. Below is an extract from a topology file (it describes the CTAC surfactant).
I am trying to convert this into a DL_POLY FIELD file (I am not a GROMACS user) but am having difficulty interpreting some of it, despite reading through the manual. Questions: 1. Does including pairs in the [ pairs ] directive cause the non-bonding 4-1 interactions to be INCLUDED or EXCLUDED? 2. The [ pairs ] directive includes 15-18 and 15-19 pairs, but neither of these pairs appear in any of the dihedrals together (nor in any other interaction). So what effect does it have to include them? Thanks very much for any guidance! ; -------- 8< --------------------------------------------------------------------- [ pairs ] ; ai aj fu c0, c1, ... 14 17 1 ; C3 N 15 18 1 ; C2 CN1 15 19 1 ; C2 CN2 15 20 1 ; C2 CN3 [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... 17 16 19 18 2 35.3 334.8 35.3 334.8 ; imp N C1 CN2 CN1 4 3 2 1 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 ; dih C13 C14 C15 C16 5 4 3 2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 ; dih C12 C13 C14 C15 6 5 4 3 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 ; dih C11 C12 C13 C14 7 6 5 4 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 ; dih C10 C11 C12 C13 8 7 6 5 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 ; dih C9 C10 C11 C12 9 8 7 6 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 ; dih C8 C9 C40 C11 10 9 8 7 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 ; dih C7 C8 C9 C40 11 10 9 8 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 ; dih C6 C7 C8 C9 12 11 10 9 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 ; dih C5 C6 C7 C8 13 12 11 10 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 ; dih C4 C5 C6 C7 14 13 12 11 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 ; dih C3 C4 C5 C6 15 14 13 12 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 ; dih C2 C3 C4 C5 16 15 14 13 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 ; dih C1 C2 C3 C4 17 16 15 14 1 0.0 5.9 3 0.0 5.9 3 ; dih N C1 C2 C3 15 16 17 20 1 0.0 3.8 3 0.0 3.8 3 ; dih C2 C1 N CN3 ; -------- 8< --------------------------------------------------------------------- -- View this message in context: http://gromacs.5086.x6.nabble.com/Interpreting-dihedrals-in-topology-file-tp5010674.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
