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

[Mark Abraham]

On 27/09/2011 12:49 PM, Liu, Liang wrote:
> 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.

"Always" is too strong, but this is common.

> Is it possible to fulfill the position restraint during Position 
> Restrained MD? Thanks.

Yes, hence the name. How well they can be fulfilled depends on the 
initial and simulation conditions.

Mark

>
> On Mon, Sep 26, 2011 at 4:56 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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 <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>
>
>
>
> -- 
> Best,
> Liang Liu
>
>

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