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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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