On 14/03/2012 5:45 AM, James Starlight wrote:
Mark,
Anything else you've known and understood about distance restraints in
some unknown context doesn't matter. What's written in the GROMACS
manual matters for using them in GROMACS :-)
So because I'm not quite understood those equations I could not
properly define my restrains (wich are in the form presented in mu
example in previous message) in accordance to the form presented in
Gromac's manual. i think it'll be kindly from you to provide the
Gromacs restrain section
(http://www.gromacs.org/Documentation/How-tos/Distance_Restraints)
with some more detailed example of application of such disres. It's
not quite understtod how the values 0 0.3 and 0.4 are correspond to
the real restrains wich would be obtained from experimental data (
Commonly it's single value of the some range like 0.4<R<0.5 )
If you can't understand the equation, plot the function by hand for
those values 0, 0.3 and 0.4. Then you will see that this shape is not
really what you want, and know what to do to make it closer to what you
do want.
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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