[gmx-users] Interpreting dihedrals in topology file

[Justin Lemkul]

On 8/22/13 1:47 PM, rdwducl wrote:
> 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?
>

Neither.  The value of nrexcl in the topology dictates which interactions are 
excluded.  See manual section 5.3.4 for a complete description of [pairs] and 
how the directive functions in the context of each force field.

> 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?
>

The end effect depends on which force field you're using; again, see manual 
section 5.3.4.

-Justin

> 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.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================