Justin,<br><br>1) I've already tried to examine this graphs but have not understood the meaning of the Ro value.<br><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>
<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>
<br><br>James<br><br><div class="gmail_quote">13 марта 2012 г. 17:19 пользователь Justin A. Lemkul <span dir="ltr"><<a 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>
==============================<u></u>==========<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 href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
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