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Hi

I'm performing NVT MD on 19 atoms with SMASS=0 and time step 5fs. I want to calculate the instantaneous temperature of one particular atom in the system. The way I'm calculating it is

I get the distance travelled by the atom from t(0) to t(5fs) say q

Then I calculate the parameter s at each time step by

s=exp(SP/gkT) where SP is the potential energy of the thermostat, g= degree of freedom, k=Boltzmann constant and T is the set temperature in the simulation

then the real time dt = virtual time(which is 5fs)/s

then velocity v= q/real time(which is dt)

Finally the instantaneous temperature of the atom = mv^2/k*g

Is the calculation right because I'm getting unrealistic numbers.
I read the Nose paper and I could not find an answer.
Suggestions will be appreciated!

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