Hi Afsaneh,
The PBC and the .gro file format are explained in the manual, chapter 3.
The last line of the .gro file has the box stored as
XX YY ZZ XY XZ YX YZ ZX ZY
Cheers,
Tsjerk
On Mar 5, 2011 6:03 AM, "afsaneh maleki" <maleki.afsa...@gmail.com> wrote:
Hi,
I want to create *.gro file with simulation box size as following:
3.4604674520000 0.000000000000 0.000000000000
1.7302337260000 2.9968527222000 0.000000000000
0.000000000000 0.000000000000 10.0000000000
I used the command:
]editconf –f *.pdb –o *.gro –box 3.46 3.46 10. –c –angle
90 90 60
are these commands proper to create this simulation box size?
system size : 4.975 2.951 0.084 (nm)
center : 0.025 0.548 0.966 (nm)
box vectors : 0.000 0.000 0.000 (nm)
box angles : 0.00 0.00 0.00 (degrees)
box volume : 0.00 (nm^3)
shift : 2.570 0.951 4.034 (nm)
new center : 2.595 1.498 5.000 (nm)
new box vectors : 3.460 3.460 10.000 (nm)
new box angles : 90.00 90.00 60.00 (degrees)
new box volume : 103.68 (nm^3)
Also I paste some .gro file
1 NAU 39 1.759 1.647 4.998
1 HAC 41 1.855 1.618 4.993
1 HAB 40 1.686 1.578 5.002
3.46000 2.99645 10.00000 0.00000 0.00000 1.73000 0.0000
-0.0000 -0.00000
What is three last values in box vector,0.00 -0.00 -.0 0?
Would one please clear me about these vectors?
3.46000 2.99645 10.00000 0.00000 0.00000 1.73000 0.0000
-0.0000 -0.00000
xx yy zz ? ?
xy ? ? ?
I have another question that does g_hbond has the compatibility with
non-cubic (or parallelpiped) cells?
good luck
Afsaneh
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