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">On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S <span dir="ltr"><<a href="mailto:mssulatha@gmail.com">mssulatha@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">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>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br>