[gmx-users] periodic boundary box

[Justin A. Lemkul]

Qian Wang wrote:
> 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?
>  

What you're seeing is entirely normal:

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

> 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?
>  

Most Gromacs tools deal with PBC intrinsically, so g_dist may not need this 
correction to work properly.  Run an analysis with and without PBC correction to 
convince yourself.

Lots of periodic jumps may confuse g_wham, but I don't know offhand.  It is 
probably preferable to avoid such jumps during mdrun to avoid bad interpretation 
of PBC, but without a lot more information about how you set up your system, 
there's not much more to say.  There is a tutorial linked from the Gromacs site 
that explains a reasonable method for preparing a pulling system.

-Justin

> Thanks a lot.
>  
> Best,
> Qian
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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