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

Liu, Liang liu4gre at gmail.com
Tue Sep 27 16:21:47 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.



perfect, thanks a lot.

Does this conflict with the bond restraint, e.g. LINCS algorithm,
during simulation?

Liang Liu
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