[gmx-users] rhdo box shape changed during simulation
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)
the last line in the gro file changed to:
8.95030 8.95030 6.32914 0.00000 0.00000 0.00000 0.00000 -
what does the last two negative values exactly mean?
Thanks for any help!
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