Am 07.05.2010 16:03, schrieb David van der Spoel:
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 :).
Hi David,
thanks for your reply.
Well, for all the other 10 dihedrals (alcohols, ethers, acetals,
carbohydrates) in the reference from 1997 (see above) my results match
:). It's just the three hydrocarbon related ones that were significantly
off.
So I guess it's likely that exactly these parameters were changed at
some point in between, although van Gunsteren still used them in 2002
(see above).
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
The one I am talking about is
CT CT CT HC 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 ; hydrocarbon all-atom
which was also used for
CO CT CT HC 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 ; acetal
and
CT CT CO HC 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 ; acetal
amongst others ...
Except for the factor 2 in C3 these are very much consistent with your
result, so maybe you just missed the 2 in C3 = -2 F3 in Eqn 4.64?
So I am lost here...
--
Markus Tusch M.Sc.
University of Paderborn
Faculty of Science
Department of Chemistry
Warburger Str. 100
D-33098 Paderborn
Germany
Tel. +49-5251-60-5754
e-mail mtu...@mail.upb.de
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