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

[Justin Lemkul]

On 12/30/19 11:11 PM, sunyeping wrote:
> Hello Justin,
>
> Thank you for your reply.
>
> If I need to prove the repeatability of a phenonmenon (such as the 
> peptide folding pathway or a conformational transition) in 
> simulations, is it reasonable to run the production MD several times 
> and each time the simulation is continued for the same NPT 
> equilibration? Do I need to introduce centain random factors (if not 
> the velocity) in each production simulation?
>

No, because those aren't independent observations. You're just running 
the same .tpr file over and over again, which will diverge slightly for 
numerical reasons but these are not true replicate simulations. If you 
want to prove repeatability, you need to repeat exactly what you did in 
the first case multiple times, with the only difference being either (1) 
a different initial configuration or (2) the same configuration with 
different initial velocities. The initial condition is what needs to 
change, and then you need to equilibrate and perform the simulation the 
same way to see if the same behavior arises.

-Justin

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Justin A. Lemkul, Ph.D.
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