[gmx-users] Generation of the Distance Restraints

James Starlight jmsstarlight at gmail.com
Wed Mar 14 07:50:27 CET 2012

Mark, thanks for explanation.

So if I understood that graph correctly 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 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<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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