Dear Amber users,
I intended to investigate peptide associations via MD simulation, so
I put 7 peptides in a truncated octahedron box with 30A hydration
layer. But, as I visualized my simulation in VMD, I realized that some
of my peptides moved to the edge of the box and then jumped to the
other side.
Therefore, I have tested several commands in cpptraj such as _center
with autoimage _and set all peptides in the atom mask in order to
solve this problem. But again those peptides keep jumping from one
side to the other.
I would be so much appreciated if somebody could help me to tackle
this problem.
Here is my command used in cpptraj:
1.parm x.prmtop
trajin prod.mdcrd
autoimage fixed :1-238 origin familiar
center
2.parm
trajin
center :1-238 mass origin
image origin familiar
3.parm
trajin
image familiar com :1-238
Best regards,
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Received on Sun Apr 22 2018 - 13:00:02 PDT
