[gmx-users] Generation of the Distance Restraints

[Mark Abraham]

On 14/03/2012 8:39 PM, James Starlight wrote:
> 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 (yet$
> 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 section.

You're probably doing something wrong, but in the absence of a command 
line and your .top file fragment, we can't possibly know.

>
> 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 ?

Simpler, but not a restraint to within a region. The manual section we 
are discussing links you to the available documentation elsewhere in the 
manual. I don't have the time to help with every interpretation question 
you might have.

Mark

>
> Thanks for help again,
>
>
> James
>
> 14 ????? 2012 ?. 10:50 ???????????? James Starlight 
> <jmsstarlight at gmail.com <mailto:jmsstarlight at gmail.com>> ???????:
>
>     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 ????? 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.
>                 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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