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On 9/02/2011 4:48 PM, sulatha M. S wrote:
<blockquote
cite="mid:AANLkTinVOYicR=7Hg-373gaOQmyX-us7TZSoz+Hn31B1@mail.gmail.com"
type="cite">I looked at the the paper published in 1999, (
Jorgensen et al JACS, 121, 20, 4831, 1999), the aliphatic
torsional parameters are the same as those from 1996. here are the
values,<br>
<br>
<br>
V1
V2 V3 (kcal/mol)<br>
CT-CT-CT-CT 1.740
-0.157 0.279<br>
<br>
HC-CT-CT-CT 0.000 0.000
0.366<br>
<br>
HC-CT-CT-HC 0.000 0.000
0.318<br>
<br>
<br>
Values calculated from the equation given in p.62 of the manual in
kJ/mol are <br>
</blockquote>
<br>
I can see nothing relevant on p62 of the 4.5 manual. When giving
references to literature that exists in multiple versions, please be
very precise. Giving details such as the manual version number, page
number, equation number and description of the relationship
described in the equation will make it much more likely that someone
will (want to) (be able to) help you.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTinVOYicR=7Hg-373gaOQmyX-us7TZSoz+Hn31B1@mail.gmail.com"
type="cite"><br>
c0 c1
c2 c3<br>
CT-CT-CT-CT 3.56686 -1.88907
0.65688 -2.33467<br>
<br>
HC-CT-CT-CT 0.66526 1.99577
0.000 -2.66102<br>
<br>
HC-CT-CT-HC 0.76567 -2.29702
0.000 -3.06269<br>
<br>
and the values given in ffoplsaabon.itp are:<br>
<br>
CT-CT-CT-CT 2.9288 -1.4644
0.2092 -1.6736<br>
<br>
HC-CT-CT-CT 0.6276 1.88280
0.000 -2.5104<br>
<br>
HC-CT-CT-HC 0.6276 1.8828
0.000 -2.5104<br>
<br>
So there is a difference. Which of these is correct ? Any help is
highly appreciated.<br>
<br>
Sulatha<br>
<br>
<br>
<br>
<div class="gmail_quote">
On Tue, Feb 8, 2011 at 7:48 PM, Andrew Paluch <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:apaluch@nd.edu">apaluch@nd.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid
rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left:
1ex;">
There is no error. The alkane dihedral parameters were updated
in 1999, and differ from those originally published in 1996.<br>
<br>
Andrew<br>
<br>
<div class="gmail_quote">
<div>
<div class="h5">On Tue, Feb 8, 2011 at 5:20 AM, sulatha M.
S <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:mssulatha@gmail.com" target="_blank">mssulatha@gmail.com</a>></span>
wrote:<br>
</div>
</div>
<blockquote class="gmail_quote" style="border-left: 1px
solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex;
padding-left: 1ex;">
<div>
<div class="h5">Hi all,<br>
<pre>Hi</pre>
<pre> </pre>
<pre>I've converted the OPLS-AA torsional potential parameters for the</pre>
<pre>alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation),</pre>
<pre>C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the</pre>
<pre>OPLS format given in Jorgensen et al, JACS 118, 11225 (1996) </pre>
<pre>to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found</pre>
<pre>that the calculated values are different.</pre>
<pre> </pre>
<pre>A previous post to the gmx-users mailing list on March 27, 2008,</pre>
<pre>pointed out this issue for the H-C-C-H torsional potential but there was no response to that.</pre>
<pre> </pre>
<pre>Does anyone know if there is an error in the ffoplsaabon.itp file? Or</pre>
<pre>is there a newer set of OPLS-AA parameters?</pre>
<pre> </pre>
<pre>For the OPLS-AA parameters (in kcal/mol), I used:</pre>
<pre> </pre>
<pre>dihedral<span> </span>V1<span> </span>V2<span> </span>V3</pre>
<pre>C-C-C-C<span> </span>1.740<span> </span>-0.157<span> </span>0.279</pre>
<pre>C-C-C-H<span> </span>0.0<span> </span>0.0<span> </span>0.366</pre>
<pre>H-C-C-H<span> </span>0.0<span> </span>0.0<span> </span>0.318</pre>
<pre> </pre>
<pre>from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as:</pre>
<pre> </pre>
<pre>dihedral<span> </span>C0<span> </span><span> </span>C1<span> </span>C2<span> </span>C3</pre>
<pre>C-C-C-C<span> </span>3.56686<span> </span>-1.889076<span> </span>0.65688 <span> </span>-2.33467</pre>
<pre>C-C-C-H<span> </span>0.66526<span> </span>1.99577<span> </span>0.0<span> </span>-2.661024</pre>
<pre>H-C-C-H<span> </span>0.76567<span> </span>-2.29702<span> </span>0.0<span> </span>-3.06269</pre>
<pre> </pre>
<pre>the parameters in the ffoplsaabon.itp file are:</pre>
<pre> </pre>
<pre>dihedral<span> </span>C0<span> </span>C1<span> </span>C2<span> </span>C3</pre>
<pre>C-C-C-C<span> </span>2.9288<span> </span>-1.4644<span> </span>0.2092<span> </span>-1.6736</pre>
<pre>C-C-C-H<span> </span>0.6276<span> </span>1.88280<span> </span>0.0<span> </span>-2.5104</pre>
<pre>H-C-C-H<span> </span>0.6276<span> </span>1.8828<span> </span>0.0<span> </span>-2.5104</pre>
<br>
<br>
Thankyou for any clarification.<br>
<font color="#888888"><br>
Sulatha<br>
</font><br>
</div>
</div>
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