Janne Hirvi wrote:
Hello!
I am trying to generate center of mass velocity to a water droplet so that I
could study the effect of impact velocity in the collision with a solid
surface.
First, I simply tried to generate extra velocity and compensate the increase in
temperature by decreasing other velocity components. However at the beginning
of the collision simulation temperature increased by value which corresponds
approximately to the temperature increase due to extra velocity. This is
probably due to poor equilibrium when other velocities are scaled. Temperature
coupling will equilibriate temperature but at the same time generated center of
mass velocity decreases.
Then I tried to to accelerate a single droplet in vacuum with temperature
coupling so that I could extract "equilibrium" droplets in 300K with wanted
velocities and tranfer these droplets on the studied surfaces. However I still
have a problem with temperature. When I use g_energy, droplet temperature is
wanted 300K but g_traj informs that temperature is much higher when I take into
account constrained freedoms by multiplying with 1.5 (rigid SPC). Temperature
given by g_traj actually equals to temperature given by g_energy when I
transfer the droplet on a surface for collision simulation and remove
accelaration.
I am not sure what is happening and would be pleased if I get some clarification
and maybe other suggestions how to generate center of mass velocity for
specific temperature.
Thanks,
Janne
If the droplet has an overall velocity you should probably not count
that in the temperature, i.e. you would equilibrate the droplet at a
certain temperature and then add a velocity in one direction on top of
that. There is no ready tool for that, but you could quite easily write
a perl script that does it.
If you want the net velocity to count in the temperature of the cluster
you will reduce the internal temperature in the cluster, it might even
freeze.
You can think of it as a falling raindrop. The temperature of the
raindrop is not affected by the falling because of the collision with
air keep the temperature and the friction with air compensates the
gravity force.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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