<br clear="all"> Igor Marques<br>
<br><br><div class="gmail_quote">On Tue, May 17, 2011 at 9:42 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
<br>
Igor Marques wrote:<br>
<br>
<snip><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
2. Can you post your .ndx file?<br>
for sn1 chain:<br>
<br>
Reading structure file<br>
Going to read 1 old index file(s)<br>
<br>
</blockquote>
<br></div>
Not exactly what I was going for (I wanted to see the contents of the .ndx file), but...<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
0 C12_&_r_1-72 : 72 atoms<br>
1 C29_&_r_1-72 : 72 atoms<br>
2 C30_&_r_1-72 : 72 atoms<br>
3 C31_&_r_1-72 : 72 atoms<br>
4 C32_&_r_1-72 : 72 atoms<br>
5 C33_&_r_1-72 : 72 atoms<br>
6 C34_&_r_1-72 : 72 atoms<br>
7 C35_&_r_1-72 : 72 atoms<br>
8 C36_&_r_1-72 : 72 atoms<br>
9 C37_&_r_1-72 : 72 atoms<br>
10 C38_&_r_1-72 : 72 atoms<br>
11 C39_&_r_1-72 : 72 atoms<br>
12 C40_&_r_1-72 : 72 atoms<br>
13 C41_&_r_1-72 : 72 atoms<br>
14 C42_&_r_1-72 : 72 atoms <br>
</blockquote>
<br></div>
Here you only have 15 carbons. The sn-1 (palmitoyl) should be 16.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
for sn2 chain:<br>
Reading structure file<br>
Going to read 1 old index file(s)<br>
<br>
0 C9_&_r_1-72 : 72 atoms<br>
1 C13_&_r_1-72 : 72 atoms<br>
2 C14_&_r_1-72 : 72 atoms<br>
3 C15_&_r_1-72 : 72 atoms<br>
4 C16_&_r_1-72 : 72 atoms<br>
5 C17_&_r_1-72 : 72 atoms<br>
6 C18_&_r_1-72 : 72 atoms<br>
7 C19_&_r_1-72 : 72 atoms<br>
8 C20_&_r_1-72 : 72 atoms<br>
9 C21_&_r_1-72 : 72 atoms<br>
10 C22_&_r_1-72 : 72 atoms<br>
11 C23_&_r_1-72 : 72 atoms<br>
12 C24_&_r_1-72 : 72 atoms<br>
13 C25_&_r_1-72 : 72 atoms<br>
14 C26_&_r_1-72 : 72 atoms<br>
15 C27_&_r_1-72 : 72 atoms<br>
16 C28_&_r_1-72 : 72 atoms<br>
<br>
</blockquote>
<br></div>
And the same here - 17 groups instead of 18. I'm not familiar with the numbering, but it seems odd to jump from, e.g., C9 to C13 - are you sure your first carbon (C9) is not in the glycerol backbone rather than the ester?<div class="im">
i'll also take a careful look into this! and the numbering is just like this. don't ask! ;)<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
3. What is your command for the sn-2 chain? You cannot obtain<br>
unsaturated and saturated order parameters in the same command. You<br>
must do them separately, and the index groups are different. For<br>
instance, to get the order parameters around the unsaturation, your<br>
index file should contain only Cn-1, Cn, Cn+1, Cn+2, where Cn and<br>
Cn+1 are the C atoms joined by the double bond. Then run g_order<br>
with the -unsat option. These values can then replace the<br>
corresponding carbon positions in the g_order output of the whole<br>
sn-2 chain. If done improperly, you can get weird results.<br>
the command is actually the same with the apropriate index file...<br>
maybe this is the problem for POPC - i'll look at it carefully!<br>
<br>
</blockquote>
<br></div>
Then this is certainly a problem.<div class="im">i'll look at it with my colleague. if our problem persists, we'll get back in touch!<br></div></blockquote><div><br></div><div>thanks again! ^^ </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im">
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
4. What are the simulation conditions? Are you trying to replicate<br>
the published work? Different simulations conditions will certainly<br>
impact the structural parameters, and insufficient sampling can give<br>
weird looking curves, as well. All it might mean is that your data<br>
are not yet well-converged.<br>
NPT, surface tension of 40 dyn/cm, t=310 K, GAFF force field. the<br>
plot represents the last 10 of 150 ns of production - however, it<br>
presents the same behavior in longer (200 ns) simulations!<br>
<br>
</blockquote>
<br></div>
I'd suspect the index file(s) and/or g_order commands rather than convergence issues, in this case.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
<br>
thanks!<br>
<br>
-Justin<br>
<br>
<br>
best regards and thanks in advance!<br>
<br>
Igor Marques<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></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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</div></blockquote><div><div></div><div class="h5">
<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 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.vt.edu/Pages/Personal/justin</a><br>
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