Hi all gromacs users,<br> I am simulating a protein in explicit solvent with Periodic boundary condition and PME . The box type I used <br>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 :
<br> CRYST1 90.093 90.093 90.093 60.00 60.00 90.00 P 1 1<br>which is a perfect rhdo box.<br> <br>During the simulation, it changed to:<br>CRYST1 89.503 89.503 68.425 105.59 105.59 90.00 P 1 1
<br>,which is not rhdo. <br>Meanwhile, the distance between the protein and its nearst image decreased dramatically, (they even touched).<br>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)
<br><br>And also, <br>the last line in the gro file changed to:<br>8.95030 8.95030 6.32914 0.00000 0.00000 0.00000 0.00000 -1.83879 -1.83879<br>what does the last two negative values exactly mean?<br><br><br>
Thanks for any help!<br>Liang<br>