[gmx-users] 5xRe: Impact velocity

Janne Hirvi janne.hirvi at joensuu.fi
Thu Feb 22 18:39:56 CET 2007

```Hi Bob!

Trjconv with fit-option will remove the COM motion of the droplet so that I
actually see surface approaching the droplet whose COM is kept fixed. I think
that the whole system is just centered always so that COM of the droplet stays
fixed. The trajectory still includes translational motion in droplet velocities
and g_traj gives temperature which corresponds to sum of thermal motion and
translational motion. I suppose that mdrun -rerun will give the same solution
for the new trajectory but I still have to test it tomorrow...

Janne

> So, does g_traj really give you a trajectory that has the COM velocity
> of the droplet removed? It looks like this is what you were trying to
> do, but I just wanted to be clear on the outcome.
>
> If that is the case you can do an mdrun -rerun no-com-traj.trr. This
> will feed your COM removed trajectory to mdrun and will recalculate
> the energies (including temperature).
> Bob
>
> On 2/22/07, Janne Hirvi <janne.hirvi at joensuu.fi> wrote:
> > Hi!
> >
> > Still one check because g_traj even with com -option actually gives total
> > temperature not the center of mass temperature as you agreed at the end of
> > recent reply. So you mean that I should use g_traj to extract the center
> of
> > mass velocity (or translation energy) and calculate the contribution to
> total
> > temperature (or kinetic energy) with equation
> >
> > 0.5*m(total)*v(COM)^2=0.5*N(df)*k*T
> >
> > and just substract it to be able to calculate thermal motion temperature?
> Is
> > this the same procedure what is done when temperatures are written in .edr
> > -file when acceleration is used together with temperature coupling while
> > temperature given by g_energy is smaller than the one given by g_traj?
> >
> > Thanks for your time and help,
> >
> > Janne
> >
> >
> > > Janne Hirvi wrote:
> > > > 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)?
> > >
> > > Maybe trjconv does not modify the center of mass velocity.
> > >
> > > What you can do is from your original trajectory calculate the center of
> > > mass temperature with g_traj and subtract that from the normal T. You
> > > may have to be careful with degrees of freedom.
> > >
> > > >
> > > > 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?
> > >
> > > g_energy does not do any processing of data, just reading the energy
> > > file and printing it.
> > > g_traj calculates T using above equation.

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