On 5/7/10 8:45 AM, Markus Tusch wrote:
Hi everybody,
I've just compared the following opls-aa torsional parameters for
hydrocarbons given in J. Comp. Chem., Vol. 18, No. 16, 1955 - 1970 (1997)
as well as in J. Comp. Chem., Vol. 23, No. 15, 1416 - 1429 (2002)
with those in ffoplsaabon.itp (Gromacs 4.0.7):
##literature (these are also the original values for alkanes published
by Jorgensen in 1996 I believe):
V1 V2 V3
H-C-C-H 0.0 0.0 0.318
H-C-C-C 0.0 0.0 0.366
C-C-C-C 1.74 -0.157 0.279
##ffoplsaabon.itp, keyword "hydrocarbon", (translated according to eq.
4.64 of the manual):
V1 V2 V3
H-C-C-H 0.0 0.0 0.300
H-C-C-C 0.0 0.0 0.300
C-C-C-C 1.299 -0.05 0.200
There's obviously a difference.
Is there another source for the latter parameters which I just wasn't
able to find? I know that the numbers in Gromacs were updated in 1999.
Cheers,
Markus
Hi Markus,
Erik Lindahl made those conversions based on a file provided by
Jorgensen. This did not make it into gromacs before 3.1 which was well
after 1999, but there was a downloadable force field earlier.
Now the question is whether
- the OPLS force field changed after 1996 when this was published
- Erik made an error when converting to Ryckaert Bellemans
- You made an error when converting back :).
Looking at the ffoplsaabon.itp file I can not but notice that there are
more than 1 H C C C dihedrals which are all different:
C CT CT HC 3 -0.20934 -0.62802 0.0 0.83736 0.0 0.0 ;
C CT CT_2 HC 3 -0.15910 -0.47730 0.0 0.63639 0.0 0.0
C_3 CT CT_2 HC 3 -0.15910 -0.47730 0.0 0.63639 0.0 0.0
Neither of which seems to be consistent with the Eqn 4.64
Based on H-C-C-C 0.0 0.0 0.300 I would expect
H C C C 3 0.6276 1.8828 0 -1.2552 0
So I am lost here...
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[email protected] [email protected] http://folding.bmc.uu.se
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