[gmx-users] Impact velocity

David van der Spoel spoel at xray.bmc.uu.se
Fri Feb 16 13:45:31 CET 2007

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 

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 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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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