[gmx-users] applying harmonic restraint

[Justin A. Lemkul]

devawati dutta wrote:
> Dear sir
> I want to apply harmonic restraint to the entire structure by 2.4 
> kcal/mol/A and will perform energy minimization by steepest descent 
> method followed by 100 ps simulation for DNA-drug complex.I need to 
> reduce the harmonic restaint slowly to zero by decreasing the force 
> constant value. But I don't know where to decrease the force constant 
> value. Where i will reduce the value in .mdp file? How can I apply 
> harmonic restraint in whole structure?
> 

There is no automated way to decrease the force constant of a restraint.  The 
best option is to decrease it manually by using .mdp files that specify a short 
number of steps and conditionals in the topology (i.e. #ifdef statements 
triggered by the "define" keyword in the .mdp file).

-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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