Thanks. Is this position restraint same to the one "Position Restrained MD". I see some tutorial shows there are always three step to perform a simulation: Energy minimization, Position Restrained MD and MD Simulation. Is it possible to fulfill the position restraint during Position Restrained MD? Thanks.
On Mon, Sep 26, 2011 at 4:56 PM, Justin A. Lemkul <[email protected]> wrote: > > > Liu, Liang wrote: > >> Firstly I want to thank for your reply, yes, it should be position >> restraint. >> >> I don't know how to reply in the thread, actually that was my first post. >> Therefore I have to ask you here, hope it also work to you. >> >> > Simply reply to the message. The discussion needs to stay on the list. > The members are not private tutors. > > My question is how to perform a position restraint simulation with the >> heavy atom constrained to its initial position by a harmonic potential >> E=k(r-r0)^2, >> which changes with k equal to 0, 10, 20, ..., 90, 100, and so on? >> >> > You can adjust the force constant in the posre.itp file. There is no > automated way of decreasing or increasing a restraint; independent > simulations must be run on the different topologies. > > -Justin > > Thanks, and any helps will be highly appreciated. >> >> -- >> Best, >> Liang Liu >> > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- Best, Liang Liu
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