[gmx-users] Generation of the Distance Restraints
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 ?
> 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.
> 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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