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On 15/03/2012 7:06 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopxi6O8TPHBn8Hq-6Y_xDryKPkqcoGRvQsJJcLd3RhoyXA@mail.gmail.com"
type="cite">Mark, <br>
<br>
thanks again for explanation<br>
<br>
<div class="gmail_quote"><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div class="im"> <br>
</div>
The force is the negative of the derivative of the potential
with respect to the distance. So the force is also zero
between r_0 and r_1. So if you want a distance to be
restrained between 1 and 2 nm, set r_0=1 and r_1=2. That way
the force is zero if the distance is satisfactory, and
non-zero when it is not.<br>
</div>
</blockquote>
<div><br>
I'm not quite understood the restrains definition in that case
:( So in the above example the distance between 1 and 2 nm
would be restrained and in accordance to the graph the forces
will be zero.</div>
</div>
</blockquote>
<br>
The word "restrained" is ambiguous. Being in the region of zero
force can be said to have been restrained, but being outside the
region where force is action can be said to be being restrained.<br>
<br>
<blockquote
cite="mid:CAALQopxi6O8TPHBn8Hq-6Y_xDryKPkqcoGRvQsJJcLd3RhoyXA@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div> But in the range below 1 and 2 nm the forces would be
increased in quadratic progression.</div>
</div>
</blockquote>
<br>
Below 1nm and above 2nm.<br>
<br>
<blockquote
cite="mid:CAALQopxi6O8TPHBn8Hq-6Y_xDryKPkqcoGRvQsJJcLd3RhoyXA@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div> So if I understood correctly only when atoms are not in
the desired distance range forces will occur that must bring
atoms to the desired distance. This is the opposite to the
position restrains where the forses are constant to prevent
movement of the atoms. Does it correct?<br>
</div>
</div>
</blockquote>
<br>
The forces in PR are not constant. See manual 4.3.1. The forces act
in each case to return the distance/displacement to the region/point
of zero force. A GROMACS position restraint is exactly like a
GROMACS distance restraint to the original position with r_0==r_1
and r_2 infinite.<br>
<br>
<blockquote
cite="mid:CAALQopxi6O8TPHBn8Hq-6Y_xDryKPkqcoGRvQsJJcLd3RhoyXA@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div>
</div>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div><br>
</div>
</blockquote>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> I leave the choice of
r_2 to you as an exercise </div>
</blockquote>
<div><br>
So as I understood the forces occured after r_2 threshold must
be extremely hight in comparison to gradually parabolic rise
in the two others thresholds. In what exacly cases this rapid
increase must be usefull in comparison to the gradually
parabolic manner?<br>
</div>
</div>
</blockquote>
<br>
A linear rise of the potential above r_2 is *more* gradual than a
parabolic rise in the limit of large r, which is the important part,
as Fig 4.13 makes clear... You still might be confusing potential
and force in your mind. Get that clear :-)<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopxi6O8TPHBn8Hq-6Y_xDryKPkqcoGRvQsJJcLd3RhoyXA@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div>
<br>
Thanks again<br>
<br>
James<br>
</div>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><span class="HOEnZb"><font
color="#888888"><br>
<br>
Mark</font></span>
<div>
<div class="h5"><br>
<br>
<blockquote type="cite"> 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 ?<br>
<br>
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 ?<br>
<br>
<br>
JAmes<br>
<br>
<div class="gmail_quote">14 марта 2012 г. 3:42
пользователь Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span>
написал:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
<br>
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.
<div> <br>
<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex"> <br>
<br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex"> I already
answered this.<br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/pipermail/gmx-users/2012-March/069301.html"
target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2012-March/069301.html</a><br>
</blockquote>
I've found only theoretical explanation of
such possibility (<br>
gradually increasing force constant during
simulation). But I<br>
intresting in practical implementation. Could
I do it in scope of<br>
single MDrun by some options in mdm fle or
should I do step-by-step<br>
series of simulation with gradually changing
forces appplied on the<br>
disres in each MDrun?<br>
</blockquote>
<br>
</div>
Only step by step. Something like simulated
annealing is only available for temperature
variation.<br>
<br>
Mark<br>
<blockquote class="gmail_quote" style="margin:0 0
0 .8ex;border-left:1px #ccc
solid;padding-left:1ex"> <br>
<br>
James<br>
</blockquote>
<div>
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