<div class="gmail_quote"><div>Hi, Justin.<br>Thank you for your help! I was intended to reply the third question <br>after I retryed the simulation under your advice,but I haven't enough time <br>to do it. It's too late :)<br>
<br>Just now, I do a simulation. All seems ok. I will check it again.<br><br>Thank you again!<br><br>Cun Zhang<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
> >pymol b4em.pdb # I write a python script to remove the SOL molecules<br>
> in the Carbon nanotube.<br>
<br>
Are there any solvent molecules interfering with the cross-boundary bonds?<br></blockquote><div><br>No.I use pymol to remove all residues which is far from the egdes 0.7A .<br></div><div><br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
> >editconf -f b4em.pdb -o b4em.gro -box 3.8 3.8 5.614 #rebuild the box.<br>
<br>
Why are you doing this?<br></blockquote><div><br>The b4em.pdb generated by genbox have no information about box size. So I use editconf to generate it.<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
> NOTE 1 [file CNT.top, line unknown]:<br>
> The largest charge group contains 32 atoms.<br>
> Since atoms only see each other when the centers of geometry of the charge<br>
> groups they belong to are within the cut-off distance, too large charge<br>
> groups can lead to serious cut-off artifacts.<br>
> For efficiency and accuracy, charge group should consist of a few atoms.<br>
> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.<br>
><br>
<br>
Pay attention to this note. A charge group of 32 atoms is huge.<br>
</blockquote><div>So what's your suggestion about the number of a charge group? <br></div></div><br clear="all"><br>-- <br>Blog: <a href="http://blog.4message.net">http://blog.4message.net</a><br>