[gmx-users] microcanonical

karamyog singh karamyog.singh at gmail.com
Fri May 19 09:56:02 CEST 2006

I guess since after the first run, the forces between atoms is not zero(only
negligible), when i do the 2nd run, the atoms start moving under the action
of these forces and since there is no temperature scaling or pressure
scaling, we can or might see an increase in KE as in my case. So an increase
might be correct.
Am I right? Please answer this because I am an undergraduate student and
this will clear my misconception, if any. :)
Thanks in advance.

On 5/18/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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.
> Mark
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