[gmx-users] simulation with position constraint by a harmonic potential
liu4gre at gmail.com
Tue Sep 27 04:49:53 CEST 2011
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 <jalemkul at vt.edu> wrote:
> Liu, Liang wrote:
>> Firstly I want to thank for your reply, yes, it should be position
>> 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
>> 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.
> Thanks, and any helps will be highly appreciated.
>> 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
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