On 2011-03-18 08.04, Cen-Feng Fu wrote:
Dear Users,
I am trying to do some simulations for liquid benzyl alcohol and
phenylethanol. I want to use the OPLS-AA force field. However, I don't
know which parameters should be used for atoms in these two molecules.
In the ffnonbonded.itp file for OPLS-AA, which parameters (opls_xxx)
should I use. Could anyone give some suggestions? Thanks!
Check both atomtypes.atp and the above file. Then you will be able to
find out.
I' attaching benzyl alcohol. Please double check before using it.
--
----------------------------------------------------------------------
Cen-Feng Fu
Department of Chemical Physics
University of Science and Technology of China
Hefei, Anhui, 230026, P.R.China
----------------------------------------------------------------------
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
[ moleculetype ]
; Name nrexcl
benzyl-alcohol 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
1 opls_145 1 LIG C 1 -0.115 12.011
2 opls_146 1 LIG H 2 0.115 1.008
3 opls_145 1 LIG C 3 -0.115 12.011
4 opls_146 1 LIG H 4 0.115 1.008
5 opls_145 1 LIG C 5 -0.115 12.011
6 opls_146 1 LIG H 6 0.115 1.008
7 opls_145 1 LIG C 7 -0.115 12.011
8 opls_146 1 LIG H 8 0.115 1.008
9 opls_145 1 LIG C 9 -0.115 12.011
10 opls_146 1 LIG H 10 0.115 1.008
11 opls_221 1 LIG C 11 -0.055 12.011
12 opls_218 1 LIG C 12 0.2 12.011
13 opls_140 1 LIG H 13 0.060 1.008
14 opls_140 1 LIG H 14 0.060 1.008
15 opls_154 1 LIG O 15 -0.683 15.9994
16 opls_155 1 LIG H 16 0.418 1.008
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 11 1
3 4 1
3 5 1
5 6 1
5 7 1
7 8 1
7 9 1
9 10 1
9 11 1
11 12 1
12 13 1
12 14 1
12 15 1
15 16 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 6 1
1 7 1
1 10 1
1 13 1
1 14 1
1 15 1
2 4 1
2 5 1
2 9 1
2 12 1
3 8 1
3 9 1
3 12 1
4 6 1
4 7 1
4 11 1
5 10 1
5 11 1
6 8 1
6 9 1
7 12 1
8 10 1
8 11 1
9 13 1
9 14 1
9 15 1
10 12 1
11 16 1
13 16 1
14 16 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1
2 1 11 1
3 1 11 1
1 3 4 1
1 3 5 1
4 3 5 1
3 5 6 1
3 5 7 1
6 5 7 1
5 7 8 1
5 7 9 1
8 7 9 1
7 9 10 1
7 9 11 1
10 9 11 1
1 11 9 1
1 11 12 1
9 11 12 1
11 12 13 1
11 12 14 1
11 12 15 1
13 12 14 1
13 12 15 1
14 12 15 1
12 15 16 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3 c4 c5
2 1 3 4 3
2 1 3 5 3
11 1 3 4 3
11 1 3 5 3
2 1 11 9 3
2 1 11 12 3
3 1 11 9 3
3 1 11 12 3
1 3 5 6 3
1 3 5 7 3
4 3 5 6 3
4 3 5 7 3
3 5 7 8 3
3 5 7 9 3
6 5 7 8 3
6 5 7 9 3
5 7 9 10 3
5 7 9 11 3
8 7 9 10 3
8 7 9 11 3
7 9 11 1 3
7 9 11 12 3
10 9 11 1 3
10 9 11 12 3
1 11 12 13 3
1 11 12 14 3
1 11 12 15 3
9 11 12 13 3
9 11 12 14 3
9 11 12 15 3
11 12 15 16 3
13 12 15 16 3
14 12 15 16 3
; added, improper
1 11 3 2 1 180 4.6 2
3 1 5 4 1 180 4.6 2
5 3 7 6 1 180 4.6 2
7 5 9 8 1 180 4.6 2
9 7 11 10 1 180 4.6 2
11 9 1 12 1 180 4.6 2
; ring_180
1 3 5 7 1 180 4.6 2
3 5 7 9 1 180 4.6 2
5 7 9 11 1 180 4.6 2
7 9 11 1 1 180 4.6 2
9 11 1 3 1 180 4.6 2
11 1 3 5 1 180 4.6 2
--
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