[gmx-users] What is the "gen-vel" used for?

[Justin Lemkul]

On 1/2/20 8:25 PM, Sun Yeping wrote:
> Hello Justin,
>
> Your reply is very helpful. I can understand the first method for proving
> repeatablity: use a different initial configuration. But how to set the
> different initial velocities with the same initial configuration if not
> using the "gen-vel" option in the .mdp file for the production simulations?

Again, you don't generate velocities at the outset of a "production" 
simulation. You're creating a randomized system that needs to be 
re-equilibrated. Hence, velocities are only ever generated at the outset 
of the first step of equilibration. Perhaps this is just a discrepancy 
in terminology, but one cannot justifiably start a "production" 
simulation (i.e. one in which data are collected) from a totally random 
state that may not even be stable.

-Justin

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Justin A. Lemkul, Ph.D.
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