[gmx-users] equilibration: run time or number of steps?

Mark Abraham Mark.Abraham at anu.edu.au
Thu Sep 15 03:15:38 CEST 2011

On 15/09/2011 5:13 AM, Juliette N. wrote:
> Hello,
> For the equilibration one usually looks at the total energy or the 
> observable of interest to be independent of time. I wanted to figure 
> out when we are referring to equilibration which of the run time or 
> n_steps parameters are important. One could run 1,000,000 steps with 
> dt of 0.001 ps or 0.002 ps

Your use of constraints is a critical factor in determining the largest 
time step that will lead to simulation stability.


> ending up with 1 and 2 ns simulation times. Can we infer that 2 ns 
> trial is closer to equilibration or one needs to look at the n_steps 
> regardless of total run time. I hope my question in clear to receive 
> your feedback.
> Thanks,

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