On Sat, 29 Apr 2017 17:55:20 +0000
Ramin Salimi <ramin.salimi01.utrgv.edu> wrote:
> Dear Amber users
> I am trying to pull my DNA molecule through Jarzynski method.
> However, there are some things that I do not understand quite well:
>
> 1- when we equilibrate the system using the restraint to keep the
> reaction coordinate in the initial value, do we use nmropt? Because
> during the equilibration phase, I restrain the DNA using
> restraintmask option and relieve the restraint in a few steps by
> making the value of restraint_wt smaller and smaller until I remove
> the restrainmask. I am a bit confused what to do when it says to
> restrain the RC.
I am not sure what "it" you are referring to. But non-equilibrium
simulations still require you to start from a pre-equilibrated
ensemble. This means creating unbiased and, in principle, uncorrelated
starting points. So I would not know why you would want to restrain
your RC to a particular value.
> 2- when we pick a large number of frames from the equilibrated
> ensemble trajectory, do we need to strip solvent molecules to avoid
> the contribution of solvent-solute interactions, before starting SMD?
If you plan to do your simulation in solvent you will necessarily have
to continue from your equilibrated solvent starting points.
> 3- At every value of the RC, we have 'n' number of dist_vs_t files,
> then we average as such:
> D={exp(-w1/kT)+exp(-w2/kT)+........+exp(-wn/kT)}/n Then, delta F= -kT
> Ln(D) which gives the PMF at one specific value of the reaction
> coordinate. Is this method correct?
If you "pull" your system along a RC you will receive a work value for
every simulation you do. All this work values will have to be
exponentially averaged with the Jarzynski formula. So your formula
seems to be correct.
Cheers,
Hannes.
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Received on Sun Apr 30 2017 - 09:30:03 PDT
