Dear Axel,
The bad dynamics is due to the presence of the walls. The wall is there to
prevent the volume from changing as I would want the density of the system
to be constant. Apart from that, the bottom wall is also there to prevent
the atoms at z = 0 to go to negative z positions as we expect the amorphous
carbon to be deposited on top of a substrate. I think the kinetic energy
will be more stable after 100+ steps due to the temp/scale fix.
this makes no sense. if the bad dynamics is due to the walls,
then you placed them wrong (or the carbon atoms).
i repeat. using temp/rescale is a very bad idea because it doesn't
dissipate any energy. on the contrary, it enhances fluctuations in
many scenarios, which is the opposite of what you want.
I have tried using nvt fix instead of the temp rescale but the temperature
tends to fluctuates. However, with a temp/scale fix for 0.5 ps, the
the problem is not there it is because you have a bad initial setup.
also, because of the way it operates, using fix langevin instead of
temp/rescale is a far superior choice. nevertheless, you *first* have
to start from a reasonable starting configuration, i.e. adjust the walls
so that they are located at meaningful positions.
temperature will not fluctuates that much and goes to equilibrium quickly
when it comes to the nvt fix. This is true when I am using a periodic
you are mistaken there. when you use temp/rescale at a frequency
that is a divisor of the thermo output, you don't see the real temperature
of your system.
boundary condition without the presences of the wall. I agree that the
temp/scale fix is not a good way but it is thus far the only way which gives
me a quick equilibrium of the system.
you don't get an equilibrium. that is your problem. in any case
the input you posted *doesn't even get there*, so you need to
correct that first.
Instead of having the wall, I tried using the nvt fix to try to maintain the
volume. However, I think due to the simple cubic structure which is highly
unstable for carbon and the very high temperature of 5000K, the nvt fix is
not fast enough to equilibrate the system, causing an expansion of the
system which will change the density of the system. The npt fix would not be
that makes no sense as well. with fix nvt, the volume of your system
is not changed, and thus the density *cannot* change.
suitable as the boundary condition along z is not periodic. These are the
two methods I can think of to try and replace the walls at the initial
stage. However, both do not seem to work very well.
Any suggestions would be deeply appreciated. My apologies for the
inconvenience as I am very much inexperience in doing simulation work.
you are worrying about the second problem before you have solved the first.
axel.