Thank you for your reply, Lina. I did try the prodrg server before. For A molecule, there is no improper dihedral. A just has one dihedral for the head group. For B molecule, it gives improper dihedral of the tetra nitrogen. I am wondering what is the criteria or at least a guidance of what could be the best choice for the topology file. Or any choices could be right and I have to try which one provide consistent results with experiment by trial? <br>
<br>Best!<br>Xueming<br><br><div class="gmail_quote">On Sun, Nov 13, 2011 at 9:57 AM, lina <span dir="ltr"><<a href="mailto:lina.lastname@gmail.com">lina.lastname@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div></div><div class="h5">On Sun, Nov 13, 2011 at 10:26 AM, XUEMING TANG <<a href="mailto:yujan2007@gmail.com">yujan2007@gmail.com</a>> wrote:<br>
> Hi there<br>
><br>
> I am trying to build up a topology file for a tetra nitrogen molecule using<br>
> Gromos UA and OPLS UA force field. Following are the molecules.<br>
><br>
> 1. for C<br>
> |<br>
> A. C-C-C-C-C-C-C-N-C and<br>
> |<br>
> C<br>
><br>
> C<br>
> |<br>
> B. C-C-C-C-C-C-C-N-C-C-C-C-COOH<br>
> |<br>
> C<br>
><br>
> I have several questions:<br>
><br>
> For A, the first molecule, should I use improper dihedral for the N-(CH3)3<br>
> or proper dihedral for C-C-N-C with multi 3 for the head group? Is there any<br>
> differences when using different force field (GROMOS and OPLS-UA)?<br>
> For B, the second molecule, should I use improper dihedral for the N-(CH3)3<br>
> or proer dihedral for C-C-N-C with multi 2? Is there any differences when<br>
> using different force field (GROMOS UA and OPLS UA)?<br>
><br>
> The first expression about improper didedral is a planer restriction. When<br>
> read the manual it also refers to the tetrahedral structure like this tetra<br>
> nitrogen functional group. My question is when it has<br>
> really long hydrocarbon tail, I guess it will be hard to flip over to<br>
> the mirror images. Or it is not true in the simulation?<br>
<br>
</div></div>You may take one built by other server, such as<br>
<a href="http://davapc1.bioch.dundee.ac.uk/prodrg/" target="_blank">http://davapc1.bioch.dundee.ac.uk/prodrg/</a><br>
<br>
as reference, and built yourself if necessary.<br>
<div class="im">><br>
> Thank you very much!!!<br>
><br>
> Best!<br>
> Xueming<br>
><br>
><br>
><br>
><br>
><br>
</div>> --<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<br>
> <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>
><br>
<font color="#888888">--<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>
</font></blockquote></div><br>