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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