GROMACS modification: Yes(plumed v 2.6.1)
I executed a targeted MD run which cover 0-1ns, and its trajectory shows that the PBC box of the system is shrunken along with Z axis. This picture is taken at 1ns, you might notice that the blue line(PBC) is shrunken in Z axis , while it was initially cubic.
At that time (meaning 1ns,second picture) all thermodynamic/structural parameters are reasonable, but it collapse like this if I increase the value of constraints and run longer.
All thermodynamic/structural parameters goes chaos at this simulation.
My question is ;
1, what can be main reason to occur such shrinking/collapsing ?
2, how the result of TMD run is affected, if I continue it with the second picture ?
I’m guessing that too strong constraints may cause this kind of problem, but I’m not sure.!