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On 14/03/2012 5:50 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopyRL1ezKhg0GXHTwyqBSJx2Av7C1B2j7RkdjC2YGs9S8g@mail.gmail.com"
type="cite">Mark, thanks for explanation.<br>
<br>
So if I understood that graph correctly</blockquote>
<br>
You haven't. The potential is zero between r_0 and r_1. Both the
equation and graph make this clear. The potential is non-zero
outside this range. 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>
<br>
I leave the choice of r_2 to you as an exercise :-) Having
sufficient mathematical literacy to be able to interpret equation
4.77 correctly is effectively a prerequisite for attempting
molecular simulations.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopyRL1ezKhg0GXHTwyqBSJx2Av7C1B2j7RkdjC2YGs9S8g@mail.gmail.com"
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">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 class="im">
<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 class="HOEnZb">
<div class="h5">
<br>
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