> > > 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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