Justin,<br><br><br>I've applied disres on each backbone atom of my potein within cutoff distance of 1nm ( Rc=1.0 nm). I've selected this value for cutoff to decrease overall ammount of the restains in my itp file. Also such value ( 1nm) was selected because of the relatively tight packing of the alpha helices in the TM buddle of membrane protein.<br>
<br>The selected values for disre_dist, disre_up2 and disre_frac were 1, 1.2 and 0.5 nm respectually . Also I've made disres with 1 and 0 nm values but I have not noticed any difference in the resulted behaviour of the constrained system. As the consequence I have not clearly realise what exactly is the disre_frac and in what exactly cases this option could be helpfull.<br>
<br><br>This is an example of my output itp file<br><br>[ distance_restraints ]<br>; i j ? label funct lo up1 up2 weight<br> 1 5 1 0 1 0 1.64731 2.64731 1<br>
1 10 1 1 1 0 1.7326 2.7326 1<br> 1 12 1 2 1 0 1.83886 2.83886 1<br> 1 14 1 3 1 0 1.96079 2.96079 1<br>
1 15 1 4 1 0 2.03503 3.03503 1<br> 1 17 1 5 1 0 1.99007 2.99007 1<br> 1 19 1 6 1 0 2.08879 3.08879 1<br>
1 27 1 7 1 0 2.13916 3.13916 1<br> 1 29 1 8 1 0 2.27147 3.27147 1<br> 1 30 1 9 1 0 2.35793 3.35793 1<br>
<br><br>I've made 10 ns simulation of such system and observe rapid shrinking of my protein starting with first 100ps like the distances that I chose were too small and forces shrink my protein. But when I've tried larger distance value for disre_dist my protein denatured rapidly as no disres were presented.<br>
<br>So the main question is How I could specify this disre values if I want to restrain the motion of the helixes of my protein within disre value ( e.g 10 A) relatively current confrmation ?<br><br><br>James<br><br><div class="gmail_quote">
16 มะาลฬั 2012ว. 15:05 ะฯฬฺุฯืมิลฬุ Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> ฮมะษำมฬ:<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">
Dear Gromacs Users!<br>
<br>
By that moments I've completed 2 sets of simulation in high temperature<br>
<br>
1- With applied posres on the backbone atoms ( fc= 200 ).<br>
<br>
The result was- that the posres prevented motion of the helixes as the rigid bodies so I've not noticed any conformation sampling.<br>
<br>
Question : Could I observe some conformation sampling on that trajectory by means of some external tricks ? E.g extracting of the eigenvectors via PCA?<br>
<br>
</blockquote>
<br></div>
If you've restrained the position of the atoms, there's no trick that can magically give you a more desirable result. You've limited the ability of atoms to move, plain and simple.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
2 With applied network of disres applied on backbone atoms of the helix elements of my protein within Rc=1nm.<br>
<br>
</blockquote>
<br></div>
What does Rc mean here?<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
As the result of that simulation I've observed distortion of my protein wich resulted in some kind of shrinking of the helix elements.<br>
<br>
Question : How I could specify that disres more correctly ? If I've observed some kind of shrinking of my protein does it means that Rc was chosen incorectly or should I define disres in anothe manner ? ( I'have not quite understand what exatly is the R_fract and in what situation it could be useful ).<br>
<br>
</blockquote>
<br></div>
Without seeing your [distance_restraints] directive, it's impossible to comment aside from saying that if your structure distorted severely, then yes, you did something wrong. I also don't know what R_fract is.<div class="im HOEnZb">
<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>
==============================<u></u>==========<br></div><div class="HOEnZb"><div class="h5">
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