[gmx-users] Re: Justin umbrella sampling tutorial......

rama david 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.
> -Justin
>  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,
Rama David.
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