Hi David,<br>Thanks for your suggestion. Now I have complete the topology files for benzyl alcohol and phenylethanol.<br>However, I have a new doubt. In your topology file for benzyl alcohol, <br>; ring_180<br>
1 3 5 7 1 180 4.6 2<br>
3 5 7 9 1 180 4.6 2<br>
5 7 9 11 1 180 4.6 2<br>
7 9 11 1 1 180 4.6 2<br>
9 11 1 3 1 180 4.6 2<br>
11 1 3 5 1 180 4.6 2<br>is this section necessary? If I don't put this section in the file, is the results still correct?<br>Thanks!<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
> Dear Users,<br>
> I am trying to do some simulations for liquid benzyl alcohol and<br>
> phenylethanol. I want to use the OPLS-AA force field. However, I don't<br>
> know which parameters should be used for atoms in these two molecules.<br>
> In the ffnonbonded.itp file for OPLS-AA, which parameters (opls_xxx)<br>
> should I use. Could anyone give some suggestions? Thanks!<br>
Check both atomtypes.atp and the above file. Then you will be able to<br>
find out.<br>
<br>
I' attaching benzyl alcohol. Please double check before using it.<br>
><br>
> --<br>
> ----------------------------------------------------------------------<br>
> Cen-Feng Fu<br>
> Department of Chemical Physics<br>
> University of Science and Technology of China<br>
> Hefei, Anhui, 230026, P.R.China<br>
> ----------------------------------------------------------------------<br>
><br>
<br>
<br>
--<br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
-------------- next part --------------<br>
[ moleculetype ]<br>
; Name nrexcl<br>
benzyl-alcohol 3<br>
<br>
[ atoms ]<br>
; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br>
1 opls_145 1 LIG C 1 -0.115 12.011<br>
2 opls_146 1 LIG H 2 0.115 1.008<br>
3 opls_145 1 LIG C 3 -0.115 12.011<br>
4 opls_146 1 LIG H 4 0.115 1.008<br>
5 opls_145 1 LIG C 5 -0.115 12.011<br>
6 opls_146 1 LIG H 6 0.115 1.008<br>
7 opls_145 1 LIG C 7 -0.115 12.011<br>
8 opls_146 1 LIG H 8 0.115 1.008<br>
9 opls_145 1 LIG C 9 -0.115 12.011<br>
10 opls_146 1 LIG H 10 0.115 1.008<br>
11 opls_221 1 LIG C 11 -0.055 12.011<br>
12 opls_218 1 LIG C 12 0.2 12.011<br>
13 opls_140 1 LIG H 13 0.060 1.008<br>
14 opls_140 1 LIG H 14 0.060 1.008<br>
15 opls_154 1 LIG O 15 -0.683 15.9994<br>
16 opls_155 1 LIG H 16 0.418 1.008<br>
<br>
[ bonds ]<br>
; ai aj funct c0 c1 c2 c3<br>
1 2 1<br>
1 3 1<br>
1 11 1<br>
3 4 1<br>
3 5 1<br>
5 6 1<br>
5 7 1<br>
7 8 1<br>
7 9 1<br>
9 10 1<br>
9 11 1<br>
11 12 1<br>
12 13 1<br>
12 14 1<br>
12 15 1<br>
15 16 1<br>
<br>
[ pairs ]<br>
; ai aj funct c0 c1 c2 c3<br>
1 6 1<br>
1 7 1<br>
1 10 1<br>
1 13 1<br>
1 14 1<br>
1 15 1<br>
2 4 1<br>
2 5 1<br>
2 9 1<br>
2 12 1<br>
3 8 1<br>
3 9 1<br>
3 12 1<br>
4 6 1<br>
4 7 1<br>
4 11 1<br>
5 10 1<br>
5 11 1<br>
6 8 1<br>
6 9 1<br>
7 12 1<br>
8 10 1<br>
8 11 1<br>
9 13 1<br>
9 14 1<br>
9 15 1<br>
10 12 1<br>
11 16 1<br>
13 16 1<br>
14 16 1<br>
<br>
[ angles ]<br>
; ai aj ak funct c0 c1 c2 c3<br>
2 1 3 1<br>
2 1 11 1<br>
3 1 11 1<br>
1 3 4 1<br>
1 3 5 1<br>
4 3 5 1<br>
3 5 6 1<br>
3 5 7 1<br>
6 5 7 1<br>
5 7 8 1<br>
5 7 9 1<br>
8 7 9 1<br>
7 9 10 1<br>
7 9 11 1<br>
10 9 11 1<br>
1 11 9 1<br>
1 11 12 1<br>
9 11 12 1<br>
11 12 13 1<br>
11 12 14 1<br>
11 12 15 1<br>
13 12 14 1<br>
13 12 15 1<br>
14 12 15 1<br>
12 15 16 1<br>
<br>
[ dihedrals ]<br>
; ai aj ak al funct c0 c1 c2 c3 c4 c5<br>
2 1 3 4 3<br>
2 1 3 5 3<br>
11 1 3 4 3<br>
11 1 3 5 3<br>
2 1 11 9 3<br>
2 1 11 12 3<br>
3 1 11 9 3<br>
3 1 11 12 3<br>
1 3 5 6 3<br>
1 3 5 7 3<br>
4 3 5 6 3<br>
4 3 5 7 3<br>
3 5 7 8 3<br>
3 5 7 9 3<br>
6 5 7 8 3<br>
6 5 7 9 3<br>
5 7 9 10 3<br>
5 7 9 11 3<br>
8 7 9 10 3<br>
8 7 9 11 3<br>
7 9 11 1 3<br>
7 9 11 12 3<br>
10 9 11 1 3<br>
10 9 11 12 3<br>
1 11 12 13 3<br>
1 11 12 14 3<br>
1 11 12 15 3<br>
9 11 12 13 3<br>
9 11 12 14 3<br>
9 11 12 15 3<br>
11 12 15 16 3<br>
13 12 15 16 3<br>
14 12 15 16 3<br>
<br>
; added, improper<br>
1 11 3 2 1 180 4.6 2<br>
3 1 5 4 1 180 4.6 2<br>
5 3 7 6 1 180 4.6 2<br>
7 5 9 8 1 180 4.6 2<br>
9 7 11 10 1 180 4.6 2<br>
11 9 1 12 1 180 4.6 2<br>
; ring_180<br>
1 3 5 7 1 180 4.6 2<br>
3 5 7 9 1 180 4.6 2<br>
5 7 9 11 1 180 4.6 2<br>
7 9 11 1 1 180 4.6 2<br>
9 11 1 3 1 180 4.6 2<br>
11 1 3 5 1 180 4.6 2<font color="#888888"><br>
</font></blockquote><br></div>-- <br>----------------------------------------------------------------------<br>Cen-Feng Fu<br>Department of Chemical Physics<br>University of Science and Technology of China<br>Hefei, Anhui, 230026, P.R.China<br>
----------------------------------------------------------------------<br>