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

[Justin Lemkul]

On 12/30/19 10:14 PM, sunyeping wrote:
> Dear all,
>
> In the molecular dynamics parameters (.mdp option) section of the Gromacs user guide (http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html), there is an introduction of the "gen-vel" option. According to the introduction, if set to "yes",  it will generate velocities in gmx grompp according to a Maxwell distribution at temperature gen-temp, with random seed gen-seed.
>
> However I don't understand why we should need the velocities. Is it used to generate different trajectories when running similations with the same system because in each run the "gen-vol" can give a different random velocity? But will the trajectories  exactly the same if we set the "gen-vel" option to "no" ? I think that the production MD with a system should be repeated for several times in order to get convincing results, then should I set the "gen-vol" option to "yes" or "no" for these repeative MD?

gen-vel is only ever used at the outset of equilibration, when there are 
no other velocities. All you have are coordinates, but to start the 
simulation, you need velocities. At all other stages of the simulation 
protocol, gen-vel should be set to "no," otherwise you're just breaking 
the simulation by introducing a discontinuity.

> I try to set the "gen-vel" option to "yes", but when running the grommp to generate the tpr file like:
>     gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md.tpr
>
> I get the following warning and fatal error caused by the warning:
>      WARNING 1 [file md.mdp]:
>    You are generating velocities so I am assuming you are equilibrating a
>    system. You are using Parrinello-Rahman pressure coupling, but this can
>    be unstable for equilibration. If your system crashes, try equilibrating
>    first with Berendsen pressure coupling. If you are not equilibrating the
>    system, you can probably ignore this warning.
>
> Fatal error:
> Too many warnings (1).
> If you are sure all warnings are harmless, use the -maxwarn option.
>
> Does it mean that "gen-vel" is usually used for equilibrating but no for production simulation? If I am running a production simulation, should I use the -maxwarn option to ignore the warning?

Never use -maxwarn. Seriously. It's probably bad that this option even 
exists.

Think about it - you already have velocities in the checkpoint file. Why 
would you generate new velocities?

-Justin

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Justin A. Lemkul, Ph.D.
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