[gmx-users] Re: Impact velocity
janne.hirvi at joensuu.fi
Mon Feb 19 15:59:35 CET 2007
Thanks for your quick replies David and Bob!
I was icefishing all the weekend and wasnt able to comment on your suggestions
earlier but you are absolutely right that I should use NVE-ensemble and not
count overall center of mass (COM) velocity to temperature.
NVT-ensemble was just used on testing purposes so that I could understand
something what was happening but actual problem conserned temperature and
velocities. If I generate extra velocity to the center of mass of the droplet
(in equilibrium at 300K) either by my own code or using accelerating force,
temperature analyze programs in Gromacs (g_energy and g_traj) show that
temperature is much higher due to translation of COM. However, it would be nice
to somehow detect temperature due to only termal motions (without translation)
so that I could observe possible heat transfer in the collision and make sure
that there is no energy drift in NVE ensemble for other reasons (There will be
some problems while I have used plain cut-offs for LJ-interactions in earlier
NVT-simulations without impact velocity in other words just placing the droplet
on a surface).
Any comments or is it the best option to extract COM velocity with g_traj and
just make own code which substracts this translational temperature from total
> If you wanted to study a collision, why do it at constant temperature?
> Like David said, maybe you should equilibrate the droplet at 300K, add
> a center of mass velocity to the droplet, and then study the collision
> at constant energy. The real collision probably doesn't take place at
> constant temperature anyway. The surface probably heats up a little
> upon colliding with the water droplet. Anyway, Just my thoughts...
> On 2/16/07, Janne Hirvi <janne.hirvi at joensuu.fi> wrote:
> > Hello!
> > I am trying to generate center of mass velocity to a water droplet so that
> > 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
> > of the collision simulation temperature increased by value which
> > approximately to the temperature increase due to extra velocity. This is
> > probably due to poor equilibrium when other velocities are scaled.
> > 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
> > velocities and tranfer these droplets on the studied surfaces. However I
> > have a problem with temperature. When I use g_energy, droplet temperature
> > wanted 300K but g_traj informs that temperature is much higher when I take
> > account constrained freedoms by multiplying with 1.5 (rigid SPC).
> > 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
> > and maybe other suggestions how to generate center of mass velocity for
> > specific temperature.
> > Thanks,
> > Janne
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