<div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Apr 27, 2012 at 3:27 PM, Bala S <span dir="ltr"><<a href="mailto:think_beyond@aol.com" target="_blank">think_beyond@aol.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thank you for that clarification.<br>
<br>
I found that there were SOL molecules in .top file. I could run the EM now.<br>
<br>
Coming to the Solvation step, I'm facing a problem.<br>
<br>
I have made the mentioned change (0.15 to 0.375 for C) in the vdwradii.dat<br>
locally.<br>
<br>
While adding the solvent molecules, what command should I be using?<br>
<br>
I am using the usual command I use for non-membrane simulations,<br>
<br>
$ editconf -f shrinked4.gro -o shrinked4_1.gro -c -d 1 -bt cubic<br>
<br>
followed by<br>
<br>
$ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top<br></blockquote><div><br></div><div>When you mention -bt cubic, it adds a cubic water box all around your system (if you visualize you will see your entire bilayer immersed in a cubic water box like a normal protein solvation). But that is wrong. You need to add water only on either side of the lipid membrane (that is along the z-axis only). So use the -box option with editconf without using -c and -d. You can have a look at <a href="https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial">https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial</a> It is clearly mentioned over there how to go about it.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
calculation goes for long time showing a huge number of SOL molecules.<br>
<br>
I guess I'm worng somehere.<br>
<br>
Thanks.<br>
<br>
Bala S<br>
<br>
<br>
<br>
<br>
<br>
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