[gmx-users] What is the box type of output files?

[Lam Nguyen Sy]

Dear all,

I am new to Gromacs, and I am trying to simulate my
systems with octahedral box type (the option I used
for editconf was "-bt octahedral"). 
I need to know what type of box that Gromacs put the
output systems in, because I am trying to do some
translations on some molecules that are outside the
box to put them inside, so that I can correctly
compute the number of contacts.
When using VMD to visualize some output .gro or .pdb
files, I just saw a rectangular box. Furthermore, it
is said on page 12 of the GROMACS User Manual version
3.3 that "Even when simulating using a triclinic box,
GROMACS always puts the particles in a brick shaped
volume, for efficiency reason" and "So from the output
trajectory it might seem like the simulation was done
in a rectangular box." I am not clear on this point. 
There is a series of numbers at the end of my .gro
files:
4.12763   3.89157   3.37019   0.00000   0.00000  
1.37588   0.00000  -1.37588   1.94578
I guess they are the components of the box vectors.

What type of box does GROMACS usually put an output
system in? And in the case of my systems, what is the
type of box containing them in the output files?

Any help would be very useful. Thank you in advanced.

Nguyen Sy Lam


 
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