<br><br><div class="gmail_quote">On Thu, Apr 29, 2010 at 3:29 PM, Saumya <span dir="ltr"><<a href="mailto:samvygupta@gmail.com">samvygupta@gmail.com</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;">
Hi all,<br><br>I am using the pre-equilibriated layers from Tieleman. After the first energy minimization step, I removed the periodicity using trjconv. Now, in order to scale the lipid positions, I tried using Inflategro.<br>
Do I need to use strong position restraints (because that is for protein and I am just using the lipid bilayer)?<br></blockquote><div><br>You want to scale the lipid positions to what? InflateGro is used to pack the lipid molecules around a protein, but you want to simulate only lipids, so no point in using it. If you want to simulate a lipid bilayer, you can continue with one taken from Tieleman's site (but with what objective?). <br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>After the script is run, When I try doing the energy minimization, it shows unequal number of atoms in .gro and topology file. (the GRO Input has only lipid molecules where as topology files takes into account both SOL and lipid molecules). <br>
</blockquote><div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
How to remove this error?<br><br></blockquote><div><div> </div>InflateGro always removes all water (SOL) molecules. So you need to resolvate the bilayer and update your .top file accordingly. Go through the manual once.<br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">I am unable to find any tutorial that could guide through the steps and the parameters to be set while doing the simulation of only bilayers. Please suggest some tutorial. <br>
<br>Kindly guide through the steps.<br>
<br>Regards,<br><font color="#888888">Saumya<br><br>
<br>
</font><br>--<br>
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