Dear Markus,<div><br></div><div>Just a follow-up: how did it all end, were able to find the source of error (if any)?<br><br><div class="gmail_quote">2010/5/10 Markus Tusch <span dir="ltr"><<a href="mailto:mtusch@mail.upb.de">mtusch@mail.upb.de</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Am 07.05.2010 16:03, schrieb David van der Spoel:<div><div></div><div class="h5"><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
On 5/7/10 8:45 AM, Markus Tusch wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi everybody,<br>
<br>
I've just compared the following opls-aa torsional parameters for<br>
hydrocarbons given in J. Comp. Chem., Vol. 18, No. 16, 1955 - 1970 (1997)<br>
as well as in J. Comp. Chem., Vol. 23, No. 15, 1416 - 1429 (2002)<br>
with those in ffoplsaabon.itp (Gromacs 4.0.7):<br>
<br>
##literature (these are also the original values for alkanes published<br>
by Jorgensen in 1996 I believe):<br>
V1 V2 V3<br>
H-C-C-H 0.0 0.0 0.318<br>
H-C-C-C 0.0 0.0 0.366<br>
C-C-C-C 1.74 -0.157 0.279<br>
<br>
##ffoplsaabon.itp, keyword "hydrocarbon", (translated according to eq.<br>
4.64 of the manual):<br>
<br>
V1 V2 V3<br>
H-C-C-H 0.0 0.0 0.300<br>
H-C-C-C 0.0 0.0 0.300<br>
C-C-C-C 1.299 -0.05 0.200<br>
<br>
There's obviously a difference.<br>
Is there another source for the latter parameters which I just wasn't<br>
able to find? I know that the numbers in Gromacs were updated in 1999.<br>
<br>
Cheers,<br>
Markus<br>
<br>
</blockquote>
Hi Markus,<br>
<br>
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.<br>
<br>
Now the question is whether<br>
- the OPLS force field changed after 1996 when this was published<br>
- Erik made an error when converting to Ryckaert Bellemans<br>
- You made an error when converting back :).<br>
</blockquote></div></div>
Hi David,<br>
thanks for your reply.<br>
<br>
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.<br>
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).<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
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:<br>
C CT CT HC 3 -0.20934 -0.62802 0.0 0.83736 0.0 0.0 ;<br>
C CT CT_2 HC 3 -0.15910 -0.47730 0.0 0.63639 0.0 0.0<br>
C_3 CT CT_2 HC 3 -0.15910 -0.47730 0.0 0.63639 0.0 0.0<br>
<br>
Neither of which seems to be consistent with the Eqn 4.64<br>
Based on H-C-C-C 0.0 0.0 0.300 I would expect<br>
H C C C 3 0.6276 1.8828 0 -1.2552 0<br>
</blockquote>
<br></div>
The one I am talking about is<br>
CT CT CT HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; hydrocarbon all-atom<br>
which was also used for<br>
CO CT CT HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; acetal<br>
and<br>
CT CT CO HC 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; acetal<br>
amongst others ...<br>
<br>
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?<div class="im"><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
So I am lost here...<br>
<br>
</blockquote>
<br>
<br>
-- <br></div><div class="im">
Markus Tusch M.Sc.<br>
University of Paderborn<br>
Faculty of Science<br>
Department of Chemistry<br>
Warburger Str. 100<br>
D-33098 Paderborn<br>
Germany<br>
<br>
Tel. +49-5251-60-5754<br>
e-mail <a href="mailto:mtusch@mail.upb.de" target="_blank">mtusch@mail.upb.de</a><br>
<br>
-- <br></div><div><div></div><div class="h5">
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