ABF hBond

From: Charles Whidborne (charles.whidborne_at_student.adelaide.edu.au)
Date: Mon Aug 25 2014 - 02:52:45 CDT


I am trying to perform and ABF simulation on DNA to separate some strands
and get the free energy required to seperate them.I want to do this by
defining the H-bonding atoms using the colvar component 'hBond' but am
uncertain how to write the script and implement it in my simulation by
defining every h-bond interaction along the DNA strand.

I have the atom numbers for each atom involved in H-bonding (theres a total
of 60 atoms, 30 acceptors, 30 donors). Do i define the acceptors and donors
in two blocks, or does each respective donor and acceptor need to be
defined separately?

In the Collective Variables Module, it says for hBond component 'Unlike
coordNum, it requires two atom numbers, acceptor and donor to be defined'
but doesnt give any examples on how this should be written.
So far i've written;
colvarsTrajFrequency 200
colvarsRestartFrequency 2000

colvar {
   name HBondDistance

   width 0.2 # 0.1 Angst of estimated fluctuation width

   lowerboundary 1.0
   upperboundary 22.0

   hBond {
      cutoff { (4.0, 4.0, 4.0)
      acceptor {
         atomnumbers { to be assigned }
      donor {
         atomnumbers { to be assigned }

abf {
   colvars PlaneDistance
   fullSamples 500

Thanks for any help and advice in advance


This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:45 CST