[gmx-users] rhdo box shape changed during simulation

Liang Ma liang.ma.1983 at gmail.com
Thu Nov 2 18:21:23 CET 2006

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!
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