[gmx-users] 4xRe: Impact velocity
Janne Hirvi
janne.hirvi at joensuu.fi
Thu Feb 22 14:06:11 CET 2007
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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