[gmx-users] Generation of the Distance Restraints

[James Starlight]

Mark,

thanks again for explanation



> 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'm not quite understood the restrains definition in that case :( So in the
above example the distance between 1 and 2 nm would be restrained and in
accordance to the graph the forces will be zero. But in the range below 1
and 2 nm the forces would be increased in quadratic progression. So if I
understood correctly only when atoms are not in the desired distance range
forces will occur that must bring atoms to the desired distance. This is
the opposite to the position restrains where the forses are constant to
prevent movement of the atoms. Does it correct?

>
>
>
I leave the choice of r_2 to you as an exercise
>

So as I understood the forces occured after r_2 threshold must be extremely
hight in comparison to gradually parabolic rise in the two others
thresholds. In what exacly cases this rapid increase must be usefull in
comparison to the gradually parabolic manner?

Thanks again

James

>
>
> Mark
>
>
>  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 марта 2012 г. 3:42 пользователь Mark Abraham <Mark.Abraham at anu.edu.au>написал:
>
>>
>>
>> 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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>
>
>
>
>
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