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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