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On 14/03/2012 8:39 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopyhXhSq8FcWu1B6=L2NGBvik6CE8Lc9jZj32j73yLXGdQ@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
You're probably doing something wrong, but in the absence of a
command line and your .top file fragment, we can't possibly know.<br>
<br>
<blockquote
cite="mid:CAALQopyhXhSq8FcWu1B6=L2NGBvik6CE8Lc9jZj32j73yLXGdQ@mail.gmail.com"
type="cite"><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>
</blockquote>
<br>
Simpler, but not a restraint to within a region. The manual section
we are discussing links you to the available documentation elsewhere
in the manual. I don't have the time to help with every
interpretation question you might have.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopyhXhSq8FcWu1B6=L2NGBvik6CE8Lc9jZj32j73yLXGdQ@mail.gmail.com"
type="cite">
<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 moz-do-not-send="true"
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 moz-do-not-send="true"
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>
<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>
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