[gmx-users] potential on non-protein molecules

[gianluca santarossa]

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?

Thanks
Gianluca