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

[Justin A. Lemkul]

Liu, Liang wrote:
> 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?
> 

Again, restraints and (bond) constraints are different.

http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints

They both contribute to the energy and forces in the system, but there is no 
conflict, unless your starting geometry is horrendous and the restraint force 
causes LINCS to crash.  Run-of-the-mill energy minimization almost always takes 
care of this.

-Justin

-- 
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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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