[gmx-users] Generation of the Distance Restraints

James Starlight jmsstarlight at gmail.com
Wed Mar 14 10:39:48 CET 2012

It's appeared two new questions on the same topic :)

1) By the way, new error have been occured when I've tried to use
multi-core station with MPI to calculate such restrained model ( I have no
same problems on the single station )

the error

Fatal error:
Time or ensemble averaged or multiple pair distance restraints do not work
For more information and tips for troubleshooting, please check the GROMACS

What should I do to fix it ?
I've made my restrained on the basis of example presented in the manual

2) Also I've found that there is more simple way to define restraines based
on the BONDS enty in the topology file. Could you provide me with the more
information about this simpler way ?

Thanks for help again,


14 марта 2012 г. 10:50 пользователь James Starlight
<jmsstarlight at gmail.com>написал:

> 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 ?
> 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<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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