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 ----------------------------------------------------------------------------------- perfect, thanks a lot. Does this conflict with the bond restraint, e.g. LINCS algorithm, during simulation? -- Best, Liang Liu
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