[gmx-users] peptide out of box

[Mark Abraham]

Rakesh Mishra wrote:
> 
> When I run simulations on a 42 residue peptide with a box size of 2.2 nm 
> , I find that after 4 ns , the peptide comes out of the box . Is this a 
> problem as far as the accuracy of the simulation results are concerned. 
> Do the periodic conditions account for such cases? If not , is there any 
> suggestion as to how I may salvage my data without having to start all  
> over again .

The peptide can't "come out of the box" - the system is periodic. The 
numbers in the trajectory file can be such that your visualization 
software will render an image that looks like the peptide comes out of 
the box, however. Look at the man page for trjconv and choose an option 
appropriate for your situation and use that on the trajectory before 
visualizing.

By the way, a 42 residue peptide is almost certainly too large for such 
a box, even if it is a compact peptide. There are guaranteed to be many 
water molecules (or even all of them) that are having non-bonded 
interactions with two images, which is unphysical.

Mark