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. But in the range below 1 and 2 nm the forces would be increased in quadratic progression. 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><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>
<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 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 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>
<div>
<br>
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