hi<br><br><span style="font-family:arial,helvetica,sans-serif">I followed the tutorial "lysozyme in water"</span><br style="font-family:arial,helvetica,sans-serif"><br style="font-family:arial,helvetica,sans-serif">
<span style="font-family:arial,helvetica,sans-serif">I have done upto energy minimization step i.e. </span><br><font face="Arial"><font size="3"><pre><span style="font-family:arial,helvetica,sans-serif">mdrun -v -deffnm em</span><br style="font-family:arial,helvetica,sans-serif">
<br style="font-family:arial,helvetica,sans-serif"><span style="font-family:arial,helvetica,sans-serif">I have the em.gro file</span><br style="font-family:arial,helvetica,sans-serif"><br style="font-family:arial,helvetica,sans-serif">
<span style="font-family:arial,helvetica,sans-serif">Do I need to follow the next steps - equilibration, production MD and analysis </span><span style="font-family:arial,helvetica,sans-serif"> because I just wanted to do the energy minimization<br>
of my initial peptide structure?</span><br style="font-family:arial,helvetica,sans-serif"><br style="font-family:arial,helvetica,sans-serif"><span style="font-family:arial,helvetica,sans-serif">Also is it possible to convert em.gro file into a pdb file? </span><br style="font-family:arial,helvetica,sans-serif">
</pre></font></font>Thanks <br>Kumud Agarwal<br style="font-family:arial,helvetica,sans-serif"><br><div class="gmail_quote">On Tue, Jan 24, 2012 at 11:26 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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"><div class="im"><br>
<br>
kumud agarwal wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
I want to do energy minimization of a small peptide (19 residues long) file (in pdb format).<br>
<br>
Can you please tell which tutorial is best for this purpose and which force field should I use.<br>
<br>
</blockquote>
<br></div>
Any of these should be fine:<br>
<br>
<a href="http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use" target="_blank">http://www.gromacs.org/<u></u>Documentation/Tutorials#<u></u>General_GROMACS_Use</a><br>
<br>
As for the force field, there is no single "best" option. Each force field has its own sucesses and failures. You should plan to invest significant time learning about each of the force fields and deciding which is best for your application, based on known limitations and the underlying theoretical basis for it. Choosing a force field is one of the most significant steps in conducting a quality simulation.<div>
<div></div><div class="h5"><br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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