>If I solvate my GPCR into the DPPC128 system using genbox, there are only >about 50 lipids left, which I think are too few, so I want a larger starting >structure.
>According to your note, when I did step 3, loaded my DPPC183 system to VMD, >I found the edges lined up poorly, there is are gaps between two periodic >cells. I also try other system like DPPC200, DPPC150, but only the original >dppc128 system, I've equilibrated it for 2ns, have no gap between two >periodic cells. >So, I will try another starting structure, like POPC, DMPC or your POPE. But >I still can't figure out why there are gaps when using genbox to extend the >DPPC system. It's because any overlap causes an entire lipid to be removed. If you don't want to equilibrate, try exactly doubling your system size in x and y. That should work perfectly. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
