Mark, thanks for explanation.<br><br>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 ?<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">Mark.Abraham@anu.edu.au</a>></span> написал:<br>
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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">
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I already answered this.<br>
<a href="http://lists.gromacs.org/pipermail/gmx-users/2012-March/069301.html" target="_blank">http://lists.gromacs.org/<u></u>pipermail/gmx-users/2012-<u></u>March/069301.html</a><br>
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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>
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Only step by step. Something like simulated annealing is only available for temperature variation.<br>
<br>
Mark<br>
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<br>
James<br>
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