Re: ABF hBond

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Aug 25 2014 - 10:18:12 CDT

Hello Charles, please note that system force calculation (and thus, ABF) is
not available due to the particular functional form of coordNum and hBond.

Giacomo

On Mon, Aug 25, 2014 at 3:52 AM, Charles Whidborne <
charles.whidborne_at_student.adelaide.edu.au> wrote:

> Hi,
>
> 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
> hideJacobian
> }
>
> Thanks for any help and advice in advance
>
> Charlie
>

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