[gmx-users] Generation of the Distance Restraints
Mark.Abraham at anu.edu.au
Thu Mar 15 09:24:02 CET 2012
On 15/03/2012 7:06 PM, James Starlight wrote:
> 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.
The word "restrained" is ambiguous. Being in the region of zero force
can be said to have been restrained, but being outside the region where
force is action can be said to be being restrained.
> But in the range below 1 and 2 nm the forces would be increased in
> quadratic progression.
Below 1nm and above 2nm.
> 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?
The forces in PR are not constant. See manual 4.3.1. The forces act in
each case to return the distance/displacement to the region/point of
zero force. A GROMACS position restraint is exactly like a GROMACS
distance restraint to the original position with r_0==r_1 and r_2 infinite.
> 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?
A linear rise of the potential above r_2 is *more* gradual than a
parabolic rise in the limit of large r, which is the important part, as
Fig 4.13 makes clear... You still might be confusing potential and force
in your mind. Get that clear :-)
> Thanks again
>> 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 ?
>> 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
>> I already answered this.
>> 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
>> 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.
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