Thanks Chris, I really appreciate your help!<br>I've got my extended membrane system regarding your note, and now I'm testing it with my GPCR. I am still not very familiar with the script, I think it will take some time to learn.
<br><br>Thanks again!<br><br><div><span class="gmail_quote">On 9/13/06, <b class="gmail_sendername"><a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a></b> <<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca
</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">>If I solvate my GPCR into the DPPC128 system using genbox, there are only
<br>>about 50 lipids left, which I think are too few, so I want a larger starting<br>>structure.<br><br>>According to your note, when I did step 3, loaded my DPPC183 system to VMD,<br>>I found the edges lined up poorly, there is are gaps between two periodic
<br>>cells. I also try other system like DPPC200, DPPC150, but only the original<br>>dppc128 system, I've equilibrated it for 2ns, have no gap between two<br>>periodic cells.<br><br>>So, I will try another starting structure, like POPC, DMPC or your POPE. But
<br>>I still can't figure out why there are gaps when using genbox to extend the<br>>DPPC system.<br><br>It's because any overlap causes an entire lipid to be removed.<br>If you don't want to equilibrate, try exactly doubling your system size in x and
<br>y. That should work perfectly.<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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