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 <[email protected]> > 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 [email protected] > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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