[gmx-users] simulation with position constraint by a harmonic potential

[Liu, Liang]

>
> > Thanks.
> >
> > Is this position restraint same to the one "Position Restrained MD". I
> > see some tutorial shows there are always three step to perform a
> > simulation: Energy minimization, Position Restrained MD and MD
> Simulation.
>
> "Always" is too strong, but this is common.
>
> > Is it possible to fulfill the position restraint during Position
> > Restrained MD? Thanks.
>
> Yes, hence the name. How well they can be fulfilled depends on the
> initial and simulation conditions.
>

Thanks for this information.
But how to perform a harmonic potential to all the heavy atoms of RNA?
Justin said this one should be adjusted in the posre.itp file, and what I
see in the file is all 1000. Does this means k=1000 in the equation of E = k
(r-r0)^2?
Thanks.


>
> Mark
>

-- 
Best,
Liang Liu
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