[gmx-users] microcanonical

Mark Abraham Mark.Abraham at anu.edu.au
Thu May 18 18:48:32 CEST 2006

karamyog singh wrote:
> Well, I am back. Remember my first and second mdruns. In my second, 
> after stablizing my initial configuration in the 1st md run, I used cut 
> off upto 6.3 whereas the potential minima is at 0.309. 6.3 is quite 
> large a distance compared to 0.309.  In the second run, the kinetic 
> energy increases which is correct but the total energy doesnt seem to 
> remain constant even when there are 3 million steps involved.

Why is increasing KE correct?

> How is this constant energy mode? KE increases(accepted) but the total 
> never seems to be constant. I cant keep increasing my no. of steps. 
> moreover how can so many vibrations be introduced at a temp. of 0.001 K.

It's well known (as I said a few emails ago) that cut-offs in NVE will 
cause system heating - that's why people tend to use NVT if they are 
using cut-offs. Expected NVE behaviour for this sort of system as a 
function of cut-off is outside my experience, but you can use g_energy 
to judge how fast KE and thus total energy is increasing as a function 
of simulation time. If that rate varies with the cutoff, then I'd say 
there's the problem.


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