[gmx-users] 4xRe: Impact velocity

Janne Hirvi janne.hirvi at joensuu.fi
Thu Feb 22 14:06:11 CET 2007


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 


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 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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