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<
---------------------------------------------------------------------
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--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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