[gmx-users] potential on non-protein molecules

David spoel at xray.bmc.uu.se
Thu May 13 20:58:44 CEST 2004

On Thu, 2004-05-13 at 16:02, gianluca santarossa wrote:
> Dallas Warren wrote:
> > How many atoms in the simulation?  Possibility is, if there is a small 
> > number then fluctuations in the various properties is larger, since it 
> > is all meant to be a random process occurring.  Therefore, the more 
> > atoms present, the more stable things are .... ?
> >
> Actually, the system is quite small (only 1000 atoms). But I don't know 
> how to understand if my simulations have reached equilibrium.
> AFAIK, in microcanonical ensambles smaller systems reache equilibrium 
> earlier and have bigger fluctuations of istantaneous temperature than in 
> bigger systems. Is this the same in canonical ensamble?
> Is there a tool with Gromacs by which I can find the real canonical 
> temperature of my simulation, instead of the istantaneous one?

You'd have to check whether values for potential and kinetic energy are
converged. You simply take the average values once the system has
equilibrated. Note that with Berendsen coupling the fluctuations in
temperature and pressure are reduced, whiel with Nose Hoover you
introduce another bias, not on the amplitude (IIRC) but on the
periodicity of the fluctuations. That is, if you do an FFT of the
temperature fluctuations you see a peak corresponding to the coupling

Otherwise fluctuations are proportional to 1/sqrt(N) where N is the
number of atoms.

> Thanks
> Gianluca
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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