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

Yang Ye leafyoung at yahoo.com
Mon Jul 2 21:11:44 CEST 2007

On 7/3/2007 2:24 AM, Lam Nguyen Sy wrote:
> 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.
Gromacs always output the type of box you have choosen. Because VMD 
doesn't support octahedral-type of box, it simply read the first three 
numbers and set them for x-, y-, and z-dimensions. You need to use 
"trjconv -ur compact -pbc atom" to convert your trajectory as well as 
your gro or pdb file to get them correctly displayed.
> 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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