ABF simulation, free energy to remove a DNA strand

From: Charles Whidborne (charles.whidborne_at_student.adelaide.edu.au)
Date: Tue Aug 05 2014 - 01:54:14 CDT


I am running simulations on DNA in which i have equilibrated it over so
many nanoseconds and now i want to measure the free energy of separating
the strands using adaptive biasing force (ABF) in NAMD, but due to my
inexperience (and probably lack of understanding) i am having trouble
running the simulation successfully. I have done the ABF tutorials but they
dont seem to help much when I try to relate it to my problem.

In my NAMD config file i have:
colvars on
colvarsConfig Distance.in

In my Distance.in file i have set:
colvarsTrajFrequency 200
colvarsRestartFrequency 2000

colvar {
   name COMDistance

   width 0.1
   lowerboundary 1.0 -Not sure if these two boundaries are set
   upperboundary 32.0

   distance {
      group1 {
         atomnumbers { #'s for back bone of one strand }
      group2 {
         atomnumbers { #'s for backbone of second strand }

abf {
   colvars COMDistance
   fullSamples 500

I have had a couple simulations result in the partial separation of the
strands, but as far as i can tell, due to the wrapping around each other
the strand then gets 'stuck' trying to be pulled around the second
strand... Any help or advice would be great on this.


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