I have done the simulations of thermalization of the nanotube at 300K with
1. KFLAG5 Berendsen Scheme that is only rescaling of the velocities;
2. KFLAG1 that is rescaling of the forces by rescaling of the velocities;
3. KFLAG1Vcom that is KFLAG1 with subtraction of velocity of center of mass;
4. KFLAG 0 without thermostating (microcanonical ensemble). Predictor Corrector with t of 0.5
fsec is used for the integration.
I took the geometry of the nanotube which was previously thermalized with the opened ends by KFLAG
1 applying periodic boundary condition in the axis of the nanotube and subtraction of Vcom in order to
keep the nanotube not traveling in space. As we agreed in one of our previous meetings, I thermostate
only the moving atoms and do not take into account those which are frozen.
It was important to decide what kind of thermostat we are going to use. I think that we need to choose
between KFLAG1 and KFLAG5.
I present bellow the table of frequencies which were calculated using KFLAG1 and KFLAG5
mode Full After initial