[gmx-users] Generation of the Distance Restraints
Mark.Abraham at anu.edu.au
Wed Mar 14 13:10:30 CET 2012
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
> 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.
> Thanks for help again,
> 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 ?
> 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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