Hi all!
I am exploring single molecule AIMD (H2 in this case) for different purposes. The main problem that I face is temperature/rotational modes. I try to run a AIMD using NVE and NVT ensembles, but there are some problems.
For an NVE ensemble, the system starts rotating with a conserved angular moment, even if I set equal to zero the total angular moment... This disrupt the linear movement of H2 bond oscillation. The rotation couples with the bond and generates a fake two frequency oscillator. If, after the AIMD, I correct the trajectory to a zero total angular moment for all frames (simple for diatomic homonuclear molecule, but not so easy for polyatomic molecules), the oscillator recovers the single frequency motion.
For an NVT ensemble, the thermalization is so hard for few atoms... and the system is very bad behaved.
Now I try an NVE ensemble with constrain MD, fixing the Y and Z position of both atoms, and put the bond along the X direction.
&CONSTRAINT
&FIXED_ATOMS
COMPONENTS_TO_FIX YZ
LIST 1 2
&END FIXED_ATOMS
&END CONSTRAINT
I think with it, I force the MD to evolve only over the X axis... but the initial step gives me a NaN temperature and kinetic energy, no matter what initial temperature I use. I attach both files.
The output file prints:
Calculation of degrees of freedom
Number of atoms: 2
Number of Intramolecular constraints: 4
Number of Intermolecular constraints: 0
Invariants(translation + rotations): 5
Degrees of freedom: -3
Restraints Information
Number of Intramolecular restraints: 0
Number of Intermolecular restraints: 0
************************** Velocities initialization **************************
Initial Temperature NaN K
COM velocity: NaN NaN NaN
COM position: 5.669178398657 5.669178398657 5.669178398657
Angular velocity: NaN NaN NaN
*******************************************************************************
It seems, the degrees of freedom is: 3N - constrains - invariants...
Is there a way to force the MD only along one axis to avoid rotation?
Regards!