Tsjerk Wassenaar ha scritto:
Hi Alessandro,
editconf encounters a bad box in the input file and I think it first
replaces that with a standard box internally. Check the box at the end
of box.gro to see if the result is what it should be (nine numbers,
according to the specification of the rhombic dodecahedon in Chapter 3
of the manual).
Cheers,
Tsjerk
On 11/10/08, Alessandro Casoni <[EMAIL PROTECTED]> wrote:
Hi all,
when i use "editconf" to generate a dodecahedron box with the command:
editconf -f protein.gro -bt dodecahedron -o box.gro -d 0.9
the output show me the following message:
.....
WARNING 1 [file aminoacids.dat, line 1]:
Bad box in file protein.gro
Generated a cubic box 6.941 x 4.939 x 7.460
.....
what is the mean of "bad box in file"?
and why editconf generates a cubic box?
I use gromacs 4.0
regards,
Alessandro
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Thank you Tsjerk,
i appreciate your help..if i copy the last line at the end of box.gro in
my protein.gro and rerun the editconf command i obtain:
Volume: 729.043 nm^3, corresponds to roughly 328000 electrons
No velocities found
system size : 6.941 4.939 7.459 (nm)
diameter : 8.302 (nm)
center : -1.289 -0.528 4.099 (nm)
box vectors : 10.102 10.102 10.102 (nm)
box angles : 60.00 60.00 90.00 (degrees)
box volume : 729.04 (nm^3)
shift : 8.866 8.105 -0.528 (nm)
new center : 7.577 7.577 3.572 (nm)
new box vectors : 10.102 10.102 10.102 (nm)
new box angles : 60.00 60.00 90.00 (degrees)
new box volume : 729.04 (nm^3)
and the "bad box" message disappears..
Ale
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