Constrain on DNA when using ABF for protein-DNA system

From: Mehdi Bagherpour (mehdi.bpour_at_gmail.com)
Date: Thu Oct 05 2017 - 13:25:33 CDT

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Dear NAMD users,

I have done ABF simulation for my protein-DNA system. The DNA helical axis
is in X direction and the distance between COM of protein and DNA is
orthogonal to helical Axis (X), lets call Z direction.

For doing ABF I used "distanceZ" option in colvar. When I look .dcd file
both protein and DNA are going far from each-other in Z direction.
My problem is: for some reasons I need DNA to be fixed in Z direction (in
its initial position) and for that I need just protein to move far from DNA.

Is there any solution to fix this problem without using any other
constraint on DNA, and if it is NOT, what is the best way to constraint
DNA without effecting on ABF results?

Thanks,
Mahdi

• Next message: Sadegh Faramarzi Ganjabad: "convergence criterion of free energy perturbation (FEP) simulations for pKa calculation"
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