# [gmx-users] 3xRe: Impact velocity

Janne Hirvi janne.hirvi at joensuu.fi
Thu Feb 22 09:36:43 CET 2007

```Hello David and other gmx-experts!

I havent yet been able to extract thermal motion contribution for temperature
(without translation) even I tested trjconv with fit (translation) option as
you adviced. Actually, I was able to remove the center of mass translation of
the droplet (tested with g_traj -ox) but however analyze still gives the center
of mass velocity which contributes to temperature (g_traj with -ov and -ot)?

I am wondering how thermal motion contribution for temperature is extracted by
g_energy in case of acceleration combined with temperature coupling, while
g_traj seems to include also translational motion. At least g_traj temperature
is higher and almost equal to reference temperature + temperature increase due
to translational energy(0.5*m(total)*v(COM)^2)). So, I think g_traj temperature
is calculated directly from the velocities
(0.5*SUM(m(i)*v(i)^2)=0.5*N(df)*k*T), but are (1) these velocities scaled to
remove the center of mass velocity to get temperature given by g_energy or is
(2) translational energy contribution directly substracted from the total
kinetic energy? I tested the latter method and got pretty good agreement, but
not perfect, between g_energy and g_traj temperatures but is it the exact
method?

Janne

> 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.
> ________________________________________________________________________
> 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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