[gmx-users] 4xRe: Impact velocity

[Robert Johnson]

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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