[gmx-users] box size

[Tsjerk Wassenaar]

Hi,

Read a bit more carefully though. A cubic box is based on the
circumscribed sphere of the solute, dilated with the desired distance
between the solute and the wall (and it has nothing to do with
calculation of the solvation surface, which to me sounds to be related
to solvent accessible surface).

And, yes, the three numbers at the end of the .gro file give the
vector lengths for a rectangular unit cell (of which the cubic is the
regular form). And you may at some point come to your senses and use a
rhombic dodecahedron. And then you'll come to the user list again,
asking what these nine numbers mean (which is also in the manual and
in the archives of the list). And afterwards you'll try to visualize
it and come with the question why your box doesn't show up as a
rhombic dodecahedron, but rather as a rectangular (which is also
explained in the manual, chapter three, and explained many times on
the list). And you're bound to find your molecule sticking out of the
solvent, but that's not an error because you use PBC, which really is
in the manual and in the archives, as well as mentioned in the wiki.

Now, please excuse me for being a bit harsh maybe. Yet, I do not need
to answer at all, but I felt that the slight off-the-point reply
regarding the setup of the box deserved an answer. And then, being
writing already, I thought to anticipate some of the questions I see
coming. Especially these questions where one gives the answer with a
"right??" are a bit annoying, as that indicates that one is on the
right track and capable of thinking logically, implying also that it
shouldn't be a big mental leap to find the answer in one of the
sources available.

Tsjerk

On Fri, Jul 4, 2008 at 11:33 AM, Nuno Azoia <nazoia at det.uminho.pt> wrote:
> Chih-Ying Lin wrote:
>>
>> Hi
>>
>> 1. in the last row of .gro file, the three number represent the length
>> of the box on X, Y , and Z directions in nanometer.
>> Right??
>>
>
> These values represents the real dimensions of the box
>>
>> 2.  for the editconf command,
>> editconf  -d   Distance_between_the_solute_and_the_box   bt cubicsur
>> Right??
>>
>>
>
> In this case the program takes the solute and calculates the solvation
> surface. From this calculates the maximum size of this surface, add twice
> the value "Distance_between_the_solute_and_the_box" (distance in the left
> side and distance in the right side), and the total value is, in the case of
> cubic box, the size of each direction of the box (X=Y=Z).
>
> Some careful  reading of the Manual will help.
>
>
>>
>> what are the differences between the three number in the .gro file and
>> the distance in the editconf command ??
>>
>> Thanks
>> Lin
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>
>
> --
>
> Nuno Gonçalo Azoia Lopes
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623