It's appeared two new questions on the same topic :)<br><br>1) By the way, new error have been occured when I've tried to use multi-core station with MPI to calculate such restrained model ( I have no same problems on the single station )<br>
<br>the error <br><br>Fatal error:<br>Time or ensemble averaged or multiple pair distance restraints do not work (yet$<br>For more information and tips for troubleshooting, please check the GROMACS<br><br>What should I do to fix it ?<br>
I've made my restrained on the basis of example presented in the manual section.<br><br>2) Also I've found that there is more simple way to define restraines based on the BONDS enty in the topology file. Could you provide me with the more information about this simpler way ?<br>
<br>Thanks for help again,<br><br><br>James<br><br><div class="gmail_quote">14 марта 2012 г. 10:50 пользователь James Starlight <span dir="ltr"><<a href="mailto:jmsstarlight@gmail.com">jmsstarlight@gmail.com</a>></span> написал:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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" target="_blank">Mark.Abraham@anu.edu.au</a>></span> написал:<div class="im">
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><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>
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<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/<u></u>pipermail/gmx-users/2012-<u></u>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>
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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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