[gmx-users] Box size
andreamuntean at gmail.com
Fri Oct 31 11:43:07 CET 2008
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.
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