[gmx-users] Re: Impact velocity

David van der Spoel spoel at xray.bmc.uu.se
Mon Feb 19 16:39:47 CET 2007

Janne Hirvi wrote:
> 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
> temperature?
> Thanks,
> Janne
>> 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...
>> Bob
>> 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
>> 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

You can take out the overall motion by trjconv using a fit.

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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