[gmx-users] choosing box vectors

[Justin Lemkul]

On 6/14/13 4:58 PM, gromacs query wrote:
> Dear All,
>
> I have two different membrane systems (membrane with waters only) already
> with me. So I dont need to add solvent molecules.
>
> So to start with simulation I need box size (last line in gro file). I used
> following command (for both cases):
>
> editconf -f del.pdb -o del.gro -c -bt cubic
>
>
> First case details:
>
>      system size : 10.707 11.077  7.493 (nm)
>      diameter    : 14.737               (nm)
>      center      :  6.928  6.932  6.936 (nm)
>      box vectors : 10.707 11.077  7.493 (nm)
>      box angles  :  90.00  90.00  90.00 (degrees)
>      box volume  : 888.68               (nm^3)
>      shift       : -1.574 -1.394 -3.190 (nm)
> new center      :  5.353  5.538  3.747 (nm)
>

I don't see how this is possible.  You used -bt cubic, but you clearly (1) don't 
want that, because the system is rectangular and (2) a cubic box is not 
produced.  Why even use editconf?  Clearly the input .pdb file has correct box 
vectors in it already and does not require any modification.

>
>
> Second case details:
>
>      system size : 10.065 11.826  9.911 (nm)
>      diameter    : 16.459               (nm)
>      center      :  9.229  9.229  9.229 (nm)
>      box vectors : 18.459 18.459 18.459 (nm)
>      box angles  :  90.00  90.00  90.00 (degrees)
>      box volume  :6289.31               (nm^3)
>      shift       :  0.000  0.000  0.001 (nm)
> new center      :  9.229  9.229  9.229 (nm)
>

Here, there are probably erroneously large vectors written in the .pdb file already.

-Justin

>
>
> As I have solvents already so my box size as a rule should be (Maximum X -
> Minimum X), (Maximum Y - Minimum Y), (Maximum Z - Minimum Z). This indeed I
> found to be correct for my first case in which box dimensions in gro file =
> 10.707 11.077  7.493
>
> But why in my second case box dimension in gro file = 18.459 18.459 18.459.
> Surprisingly its is equal to Maximum X + Minimum X of my system and all are
> same being 18.459. Rather it should be (Maximum X - Minimum X), (Maximum Y
> - Minimum Y), (Maximum Z - Minimum Z) as in first case.
>
> Also in VMD I saw gro files. In first case pbc box completely fits the
> membrane water system but in second case pbc box is un-necessarily large as
> it is using 18.459 18.459 18.459
>
>
> I am confused why in second case it chose Maximum X + Minimum X unlike in
> first case?
>
> please suggest,
>
> thanks,
> Jiom
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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