[gmx-users] Re: Justin umbrella sampling tutorial......
ramadavidgroup at gmail.com
Mon May 28 21:49:36 CEST 2012
Thank you Justin for reply...
> More or less. The special case with what you're doing in the tutorial is
> that you have no initiating velocities in each window; you only have
> coordinates. That's why it makes sense to do a bit of equilibration in each
> window first, generating velocities and re-equilibrating the system.
> In npt_umbrella.mdp we have
>> gen_vel = yes
>> The command line in tutorial is
grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr
grompp -f npt_umbrella.mdp -c conf450.gro -p topol.top -n index.ndx -o npt22.tpr
So if I modify the process as follow, Then is the need of equilibration
(Can we skip equilibration and run production md)
use -t flag with cpt ( to give velocity of the previous run ) file
continuation = yes
gen_vel = no .
Is these alternative process is right or totally wrong..???
Please give me a valuable suggestion.
Thank you in advance.
With Best Wishes,
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