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On 14/03/2012 12:38 AM, James Starlight wrote:
<blockquote
cite="mid:CAALQopxWa0hxBSOtTa1injuf9KS+tPbvkDoB0G2aA5gTsoqqaw@mail.gmail.com"
type="cite">Justin,<br>
<br>
1) I've already tried to examine this graphs but have not
understood the meaning of the Ro value.<br>
</blockquote>
<br>
How about reading the equation on the previous page?<br>
<br>
<blockquote
cite="mid:CAALQopxWa0hxBSOtTa1injuf9KS+tPbvkDoB0G2aA5gTsoqqaw@mail.gmail.com"
type="cite"><br>
E.g I have known distance restrains for the pair of residue wich
are 1<r< 2 for instance. As I understood the R1=1 and R2=2
but what about R0 ?As I've understood this value might be
slightly less than R1 ( e.g 0.9). Does this correct and how I
could specify R0 more accuracy?<br>
</blockquote>
<br>
Anything else you've known and understood about distance restraints
in some unknown context doesn't matter. What's written in the
GROMACS manual matters for using them in GROMACS :-)<br>
<br>
<blockquote
cite="mid:CAALQopxWa0hxBSOtTa1injuf9KS+tPbvkDoB0G2aA5gTsoqqaw@mail.gmail.com"
type="cite">
<br>
<br>
2) Besides I want to know if there are possible way to gradyally
decrease force constants during MD run? E.g I want to dicrease
this value each 100ps on the desired value. Is there any way to
defind this step value in the MDP file or should I re-run mu
simulation X times started from the previous short run with bigger
forses applied?<br>
</blockquote>
<br>
I already answered this. <a
href="http://lists.gromacs.org/pipermail/gmx-users/2012-March/069301.html">http://lists.gromacs.org/pipermail/gmx-users/2012-March/069301.html</a><br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopxWa0hxBSOtTa1injuf9KS+tPbvkDoB0G2aA5gTsoqqaw@mail.gmail.com"
type="cite">
<br>
<br>
James<br>
<br>
<div class="gmail_quote">13 марта 2012 г. 17:19 пользователь
Justin A. Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
написал:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="im"><br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
Mark, Justin,<br>
<br>
Thanks for advises. Indeed I think that simple text editor
would be better sollution in my casw because of small
number of restraints.<br>
<br>
I just have a question about definition of the Distances<br>
<br>
This is the default of the restraints between atom 10 and
16.<br>
<br>
[ distance_restraints ]<br>
; ai aj type index type’ low up1 up2 fac<br>
10 16 1 0 1 0.0 0.3 0.4 1.0<br>
<br>
<br>
<br>
I'd like to restrict distance between both of that atoms
7.96 < r(Ca-Ca)< 8.41<br>
<br>
I've found that the up1 is the 7.96 and up2 is the 8.41
but how I could specify 'low' in the above table ? Should
I obtain value for the initial Ca-Ca distance between my
residues from the initial structure? How I could do it?<br>
<br>
</blockquote>
<br>
</div>
See Figure 4.13 and equations 4.79 in the manual. r0 = low,
r1 = up1, and r2 = up2.
<div class="HOEnZb">
<div class="h5"><br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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