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

Justin A. Lemkul jalemkul at vt.edu
Mon May 28 21:52:55 CEST 2012

On 5/28/12 3:49 PM, rama david wrote:
> 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..???

Using the checkpoint in this instance is wrong.  The only checkpoint you have 
accessible to you at that point is from the end of the pulling simulation and 
corresponds to the final state of the system.  Applying these velocities to the 
intermediate configurations along the reaction coordinate is likely to do weird 
and unreliable things to the trajectory.  It is more robust to run NPT and then 
data collection, or as I said before, proceed immediately to a continuous data 
collection (with gen_vel = yes!) and discard the initial few ns of data as 
equilibration.  In theory, this procedure is no different than any other 
simulation that one conducts.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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