Ok, James thank you<br><br>It seems that I should to wite some script for too many iterations e.g<br><br><font face="Arial"><font size="3"><pre>perl <a href="http://inflategro.pl">inflategro.pl</a> minimized1.gro 0.95 DPPC 0 shrinked1.gro 5 area_shrink1.dat<br>
<font face="Arial"><font size="3"><pre>grompp -f minim.mdp -c shrinked1.gro -p topol.top -o minimized2.tpr<br><font face="Arial"><font size="3"><pre>mdrun -v -deffnm minimized2<br></pre></font></font><font><font><font face="Arial"><font size="3"><pre>
perl <a href="http://inflategro.pl">inflategro.pl</a> minimized2.gro 0.95 DPPC 0 shrinked2.gro 5 area_shrink1.dat<br><font face="Arial"><font size="3"><pre>grompp -f minim.mdp -c shrinked2.gro -p topol.top -o minimized3.tpr<br>
<font face="Arial"><font size="3"><pre>mdrun -v -deffnm minimized2</pre></font></font></pre></font></font></pre></font></font></font></font></pre></font></font>......<br></pre></font></font><font><font><font><font><font><font><font><font><font face="Arial"><font size="3"><pre>
<font face="Arial"><font size="3"><pre><font><font><font face="Arial"><font size="3"><pre>perl <a href="http://inflategro.pl">inflategro.pl</a> minimized20.gro 0.95 DPPC 0 shrinked20.gro 5 area_shrink1.dat<br><font face="Arial"><font size="3"><pre>
grompp -f minim.mdp -c shrinked20.gro -p topol.top -o minimized21.tpr<br><font face="Arial"><font size="3"><pre>mdrun -v -deffnm minimized21<br><br>Does this action sequence correct? So as the consequence I need to find operator wich stop the script untill defined value of S per lipid will be reached<br>
</pre></font></font></pre></font></font></pre></font></font></font></font></pre></font></font></pre></font></font></font></font></font></font></font></font></font></font><br><br>Thanks again<br><br>James<br><br><div class="gmail_quote">
2011/10/17 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<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;"><div class="im">
<br>
James,<br>
<br>
As the consequence the correct orientation of the peptide in the membrane as well as futher solvation are caused many questions :)<br>
<br>
<br>
Firsly, following by tutorial guide I've done orientation of KALP peptide in the membrane by<br>
<br></div>
1- perl <a href="http://inflategro.pl" target="_blank">inflategro.pl</a> <<a href="http://inflategro.pl/" target="_blank">http://inflategro.pl/</a>> confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat<br>
2- minimization<br>
3- perl <a href="http://inflategro.pl" target="_blank">inflategro.pl</a> <<a href="http://inflategro.pl/" target="_blank">http://inflategro.pl/</a>> system.gro 4 DPPC 14 system_inflated.gro 5 area.dat<div class="im">
<br>
<br>
<br>
<br>
4- minimization<br>
<br>
after six iterations of the 3rd and 4th steps I've obtained 6,5 nm^2 value for the area per lipid<br>
<br>
</div></blockquote>
<br>
The tutorial suggests at least 26 or so iterations. Your APL value is 100 times larger than it should be.<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;">
Next I've done solvation of my protein ( including big vdv radii for carbons )<br>
<br>
<br>
<br>
Finally my sytem is consisted of 70000 atoms. I think that it's too big ammount of water molecules for such small protein like KALP<br>
<br>
</blockquote>
<br></div>
Yes, because your membrane is not correctly packed.<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;">
so its seems that i've done some mistakes-<br>
1- During shrinking of my peptide- I think that obtained structure (<a href="http://www.sendspace.com/file/wenkf4" target="_blank">http://www.sendspace.com/<u></u>file/wenkf4</a>) consist of too big distances beetween peptides so it should be futher shrinked.<br>
<br>
</blockquote>
<br></div>
Correct.<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;">
<br>
<br>
But how many iterations must be? I've found in the tutorial that 65 A^2 is good value for that system. But maybe I've used wrong parametries in the pl program?<br>
<br>
</blockquote>
<br></div>
No, you just haven't done enough iterations. See above. Your value is 6.5 nm^2 , which is 6500 A^2.<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- Or maybe too many waters are moved within the membrane in spite of increased VDV radius for carbon atoms. So what I should do for the excluding all unnecessary water from my structure?<br>
<br>
<br>
</blockquote>
<br></div>
Ignore this for now. Your system simply isn't built correctly.<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;">
<br>
E.g I want to simulate hydrophobic effect. What length of that simulation must be ?<br>
</blockquote>
<br></div>
Perhaps tens of ns.<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;">
How I can evaluate the ammount of water before and after simulations?<br>
</blockquote>
<br></div>
Visualization.<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;">
Finally, What other options of Genbox could I use for preventing insertion of water into my membrane ?<br>
<br>
<br>
</blockquote>
<br></div>
None. A better starting model is required.<br><font color="#888888">
<br>
-Justin</font><div><div></div><div class="h5"><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>
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