How to pull protein-Monomer from DNA using ABF without any force on DNA?

From: Mehdi Bagherpour (
Date: Tue Jun 13 2017 - 12:30:29 CDT

Dear NAMD users,

I am using the ABF simulation for protein-DNA system in NAMD. Actually I
have dimer-protein that are binding to DNA and I want to pull first monomer
of protein vertically in order to get some idea about its binding affinity
to DNA. My selected colvar is the distance between COM of first monomer and
COM of its related interacted DNA. I have use *distanceZ* option as below:

The total mass of protein monomer = 8105.1
The total mass of related DNA = 4309.73

colvarsTrajFrequency 1000
colvarsRestartFrequency 1000

colvar {

name chADistance

width 0.1 # 0.1 Angstrom of estimated fluctuation width

lowerboundary 16
upperboundary 36

lowerwallconstant 200.0
upperwallconstant 200.0
   # difference of two distances
    distanceZ {
               oneSiteSystemForce yes

               # e.(r-r1)

               axis (-13.28, -6.63, -6.3)
               # atoms of first monomer of protein
               main {
                                     atomNumbersRange 1-1093
                                     atomNumbersRange 3330-3339
               # atoms of first related DNA
               ref {
                                     atomNumbersRange 2215-2437
                                     atomNumbersRange 3073-3295

abf {
  colvars chADistance
  fullSamples 500

In simulation at first protein monomer is departing a bit from DNA (around
2 Angstrom) and then instead of protein monomer, DNA is staring to bend in
order to be apart of protein.

In fact this is not the case and I want to see the just effect of protein
leaving DNA without any force on DNA.

My question is: *Do you have any idea what can I do in ABF without putting
any external constrains on DNA in order to prevent DNA bending?*

Looking forward to hearing your ideas.


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