Hi all,
I want to perform single molecule molecular dynamics.
First I do a convergence test for cutoff, cell size and poisson solver. I read in old mails, that MT is better than WAVELET for MD, due to the first is translational invariant.
After that I start a MD from the optimized molecular geometry at the same level of theory. I want to obtain statistical information for a given temperature (300K for example), I think an NVT is not well behaved for a single molecule, then I ran NVE MD. As the geometry is at the minimum, I start with 2*T (where T is the target temperature) thinking in virial theorem (at equilibrium equal potential and kinetic energy).
But the system is not converging (the average temperature) at the desired temperature. It shows a weird temperature oscillation (different as expected due to bond oscillation), it present in some moment higher temperature than the initial and a potential energy lower than the initial... Also, the molecular rotation exhibits variations along the MD and translation in the box. For that I start a new MD with the same INPUT and geometry, adding ANGVEL_ZERO. The MD starts without rotation but in 300 fs it starts to rotate.
I attach the files for both MD.
I read about the geometrical constraints, it would be useful for diatomic molecules, but for H2O or complexer molecules is not a solution.
Has somebody faced these problems? some advice?
regards