[gmx-users] rhdo box shape changed during simulation

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Nov 2 20:26:26 CET 2006

Hi Liang,

Apparently, your system contracted in one direction. You can avoid
this by simulating at constant volume or by using isotropic pressure
Your protein should not have direct interactions with its periodic
images during the simulation. This usually means you can discard your
The last two values are the x and y skewing of the third vector
defining your periodic lattice (the periodic boundary conditions).
Likewise, the first two zeros are the y and z skewing of the first
vector and the other two zeros are the x and z skewing of the second
vector. You can check chapter 3 of the gromacs manual to get to know
more about periodic boundary conditions in gromacs.



On 11/2/06, Liang Ma <liang.ma.1983 at gmail.com> wrote:
> Hi all gromacs users,
>      I am simulating a protein in explicit solvent with Periodic boundary
> condition and PME . The box type I used
> is rhdo (rhombic dodecahedron). However, I checked the box length and angle
> during simulations,  it  deviates far away from the normal rhdo box shape.
> For example, the third line  in  pdb  at the beginning is :
>  CRYST1   90.093   90.093   90.093  60.00  60.00  90.00 P 1           1
> which is a perfect rhdo box.
> During the simulation, it changed to:
> CRYST1   89.503   89.503   68.425 105.59 105.59  90.00 P 1           1
> ,which is not rhdo.
> Meanwhile, the distance between the protein and its nearst image decreased
> dramatically, (they even touched).
> So my question is this normal? If not, is there any way to constraint the
> box always in a rhdo box shape (a=b=c)
> And also,
> the last line in the gro file changed to:
> 8.95030   8.95030   6.32914   0.00000   0.00000   0.00000   0.00000
> -1.83879  -1.83879
> what does the last two negative values exactly mean?
>  Thanks for any help!
> Liang
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Tsjerk A. Wassenaar, Ph.D.
NMR, Utrecht University,
Padualaan 8,
3584 CH Utrecht, the Netherlands
P: +31-30-2539931
F: +31-30-2537623

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