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

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 27 16:15:47 CEST 2011

Liu, Liang wrote:
>      > 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?

Yes.  See my previous message.  I explained the contents of the file, which are 
also discussed in the manual.



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


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