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.
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?
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?
I already apologize if these have been addressed. Any help is greatly appreciated.
Thanks
Ramin
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Received on Sat Apr 29 2017 - 04:30:02 PDT
