[gmx-users] error in hydrocarbon dihedrals of opls-aa?

[Vasilii Artyukhov]

Dear Markus,

Just a follow-up: how did it all end, were able to find the source of error
(if any)?

2010/5/10 Markus Tusch <mtusch at mail.upb.de>

> 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 mtusch at mail.upb.de
>
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