[gmx-users] simulation with position constraint by a harmonic potential

[Liu, Liang]

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 <jalemkul at vt.edu> 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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