[gmx-users] Box size

[Florian Haberl]

Hi,

On Friday, 31. October 2008, Andrea Muntean wrote:
> 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 pdb file the box information is normally defined in the beginning of 
the file with

CRYST1 X Y Z A1 A2 A3

box x box y box z and angle 1 2 3

>
> 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?

In the .gro file the box information is in the end of the file. 

>
> 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?

No, you need start editconf 

>
> Thank you in advance for any contribution.
>
> Best regards,
> Andrea


Greetings,

Florian

-- 
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 Dr. Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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