Re: Fixing atoms while equilibration

From: Axel Kohlmeyer (
Date: Mon Sep 01 2014 - 08:14:37 CDT

On Mon, Sep 1, 2014 at 3:07 PM, Siva Dasetty <> wrote:
> Dr.Kohlmeyer,
> Thank you again for the reply.
> I understand that the DOF=0 and so are the velocities as the atoms are
> fixed. Temperature is calculated from K.E (which is calculated by the atoms
> velocities) and DOF(0 in this case) using (T = Sum_i (m(i)*v(i)^2) /
> (n_DOF*k_B) ).
> Yes you cannot compute temperature and this is why I was confused initially
> when I saw this huge number 9999999.99 but now it somewhat makes sense as
> both numerator and denominator are zeros.
> So, does that mean this value I am seeing is equal to infinity in NAMD?

the only way to answer this in certainty would be to look it up the in
the source code. feel free to check it out.


> Thanks,
> Siva

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