[gmx-users] timestep

Erik Lindahl lindahl at stanford.edu
Mon Mar 25 17:30:08 CET 2002

David van der Spoel wrote:
> On Mon, 25 Mar 2002, Anton Feenstra wrote:
>>Rainer Boeckmann wrote:
>>>maybe that's the problem. I did in fact only change the timestep. But: how do
>>>parameters like nstlist affect the energies at step 0? The kinetic energy at step
>>>0 is different fot two runs starting from the same gro-file but with different
>>>delta t. Thought these parameters were only important for later steps...
>>>Thanks a lot,
>>I can't see any relation between nstlist and properties at step 0,
>>but dt will actually affect these. The reason is that in the trajectory
>>(or .gro file) coordinates are stored at whole time steps and velocities
>>at half. Changing the timestep will change the 'interval' between the
>>time of the velocities and the coordinates. This might give rise to some
> There is one relation: initial shake.

Another potential culprit is the temperature coupling algorithm; 
Nose-Hoover will give you a closer equilibrium temperature, but each 
time you start your simulation the dynamical heat bath variable is set 
to zero, and you might see some fluctuations before it has settled down.



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