<div class="gmail_extra">Hello Albert,</div><div class="gmail_extra"><br></div><div class="gmail_extra">Thanks.</div><div class="gmail_extra">Yes, CHARMM36 indeed handles lipids very well. But currently GROMACS 4.5.5 provides only the option for CHARMM27 FF and I found that ff43a1 very well preserves the characters of both the protein as well as the lipids for fairly long simulation time, hence I used that FF in the tutorial. But one can surely add CHARMM36 to GROAMCS by doing all the necessary topology conversions.</div>
<div class="gmail_extra"><br></div><div class="gmail_extra"><br></div><div class="gmail_extra">Regards,</div><div class="gmail_extra"><br></div><div class="gmail_extra">Anirban<br><br><div class="gmail_quote">On Thu, Apr 26, 2012 at 3:08 PM, Albert <span dir="ltr"><<a href="mailto:mailmd2011@gmail.com" target="_blank">mailmd2011@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 bgcolor="#FFFFFF" text="#000000">
it seesm to be good. <br>
just one pieces of advices, why not use CHARMM36 for this tutorial ?
since it is the best FF for lipids currently.<div><div class="h5"><br>
<br>
On 04/26/2012 11:14 AM, Anirban Ghosh wrote:
<blockquote type="cite"><span>Hi ALL,</span><br>
<div class="gmail_quote">
<div style="color:rgb(34,34,34)"><br>
</div>
<div style="color:rgb(34,34,34)">I have prepared a step-wise
tutorial for running a MD simulation of a GPCR protein
inserted in a lipid bilayer. It can be found at the following
URL:</div>
<div style="color:rgb(34,34,34)"><br>
</div>
<div style="color:rgb(34,34,34)"><a href="https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial" style="color:rgb(17,85,204)" target="_blank">https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial</a></div>
<div style="color:rgb(34,34,34)"><br>
</div>
<div>
<div>I sincerely hope it will help people who are new to such
simulations and the GROMACS community in general. This
tutorial is adapted from the membrane protein tutorial
prepared by Justin Lemkul.</div>
<div><br>
</div>
<div><br>
</div>
<div>Regards,</div>
<div><br>
</div>
<div>Anirban</div>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div></div>
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