<div dir="ltr">Thank you David,<br><br>I am about halfway through the Gromacs 2007 Workshop material. Very nice.<br>I'm wondering if there is any workshop videos covering QM/MM methods in Gromacs.<br><br>Thanks,<br><br>
Jack<br><br><div class="gmail_quote">On Sun, Oct 19, 2008 at 4:14 PM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</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;">
<div class="Ih2E3d">Jack Shultz wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
<br>
I am fairly new to GROMACS but I have spent time running tutorials for several other molecular dynamics applications. I would like to know if the current framework for GROMACS has support for methods that calculate saddle point energy in first-order reactions. If so, are there examples I can read about?<br>
</blockquote>
<br></div>
First, GROMACS does not support reactions, unless you use the QM/MM methods in which case you have to look into e.g. Gaussian's way of doing a Transition State optimization.<br>
<br>
Second, you can do normal mode analysis which would give you indirectly the needed information, if you have a conformation that you know is the transition state.<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Jack<br>
<br>
<br>
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-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
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