[gmx-users] Generation of the Distance Restraints

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 14 13:02:47 CET 2012

On 14/03/2012 5:50 PM, James Starlight wrote:
> Mark, thanks for explanation.
> So if I understood that graph correctly

You haven't. The potential is zero between r_0 and r_1. Both the 
equation and graph make this clear. The potential is non-zero outside 
this range. The force is the negative of the derivative of the potential 
with respect to the distance. So the force is also zero between r_0 and 
r_1. So if you want a distance to be restrained between 1 and 2 nm, set 
r_0=1 and r_1=2. That way the force is zero if the distance is 
satisfactory, and non-zero when it is not.

I leave the choice of r_2 to you as an exercise :-) Having sufficient 
mathematical literacy to be able to interpret equation 4.77 correctly is 
effectively a prerequisite for attempting molecular simulations.


> I must define R1=1 and R2=2 values from my example 1<Rij<2 to obtain 
> quadratic restrain forces done in my distance range ( from 1 to 2 
> angstr). In other words this would restrains the i and j atom to the 
> desired distance by the force wich would increased by the quadratic 
> progresion upon distance will increased up to 2. Does it correct ?
> So the value R0 ( no forces= no restraints) must correspond to the 
> values above and below my range. How the same range value for R0 could 
> be defined ?
> JAmes
> 14 ????? 2012 ?. 3:42 ???????????? Mark Abraham 
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> ???????:
>     I can't think of a clearer way to explain the functional form of
>     the distance restraint than the given equation with an example
>     graph of it nearby. You have some distance range that you want to
>     see happen based on some external information. You need to choose
>     the distance constants for that functional form to reproduce that
>     in a way that you judge will work, given your initial distance.
>     The linear regime above r_2 is useful for not having forces that
>     are massively large (from a quadratic potential) far from the
>     region of zero potential. Whether this is important depends on
>     your starting configuration.
>             I already answered this.
>             http://lists.gromacs.org/pipermail/gmx-users/2012-March/069301.html
>         I've found only theoretical explanation of such possibility (
>         gradually increasing force constant during simulation). But I
>         intresting in practical implementation. Could I do it in scope of
>         single MDrun by some options in mdm fle or should I do
>         step-by-step
>         series of simulation with gradually changing forces appplied
>         on the
>         disres in each MDrun?
>     Only step by step. Something like simulated annealing is only
>     available for temperature variation.
>     Mark
>         James
>     -- 
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