On 2011-03-18 12.23, Cen-Feng Fu wrote:
Hi David,
Thanks for your suggestion. Now I have complete the topology files for
benzyl alcohol and phenylethanol.
However, I have a new doubt. In your topology file for benzyl alcohol,
; 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
is this section necessary? If I don't put this section in the file, is
the results still correct?
This is for you to find out based on the original article. There may or
may not be a reference in the atomtypes.atp. Otherwise check generic
OPLS articles.
Thanks!
> 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 <mailto:sp...@xray.bmc.uu.se>
http://folding.bmc.uu.se
-------------- next part --------------
[ 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
--
----------------------------------------------------------------------
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
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