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
<jmsstarli...@gmail.com <mailto:jmsstarli...@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.abra...@anu.edu.au <mailto:mark.abra...@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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