[gmx-users] periodic boundary box

[Qian Wang]

Hi,
 
I use Gromacs4.0.5 to run a 20 ns npt simulation in periodic boundary box. At first I put peptide in the center of the box, then I write comm_mode = linear in *mdp file. However, the peptide still moves out of the box and go through to the other side of the box. Is there any method that can solve this problem?
 
Another question is that after the peptide accross the box like I said above, I think if I want to use g_dist I should use "trjconv -nojump" first. Then if I use the umbrella sampling method and use g_wham -it tpr.dat -ix pullx.dat to analyze the data. Do I need to do any other steps before I use the  g_wham command?
 
Thanks a lot.
 
Best,
Qian
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