[gmx-users] Box size

Andrea Muntean andreamuntean at gmail.com
Fri Oct 31 11:43:07 CET 2008

Hi all,

I have my box defined at the end of my pdb file as (lenghts in Angstrom)

AXAYAZt       70.0000    70.0000   112.0777  5800.0000

In the gro file (produced by pdb2gmx) I get

   2.51900   2.84400   6.80610

on the last line. Is this my box reduced to the size of the molecule?
Or what does this represent?

Should I run now editconf and define the box there (in nm)? Would
(a,b,c) (the box vector lenghts) will be the initial lenghts
(70,70,112.0777) divided by 10 (the convertion from Angstrom to nm) or
is there another rule?

Or can I specify somehow the box coordinates (vector lenghts and
angles) already when I run pdb2gmx?

Thank you in advance for any contribution.

Best regards,

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