I did the catting of lipid.gro and protein.gro and named it as system.gro and then I inflated DSPC using INFLATEGRO script command and also I am using the default value of 14A for cut off distance. So I don't have much idea that after inflating the whole system if I run the EM then protein and lipid should minimize.<div>
<br></div><div>LINCS warning originates from the very first step as I my stepsize is 1000 and dt=.03 (provided by MARTINI) and LINCS says that there are 22 inconsistent shifts and the maximum force is at atom 3373 which is 8.153704e+04. Do you have any idea?</div>
<div><br></div><div>Sunny<br><br><div class="gmail_quote">On Mon, Nov 2, 2009 at 4:49 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;">
<div class="im"><br>
<br>
sunny mishra wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi All,<br>
<br>
I am having a trouble during EM step after I inflategro my lipid.gro (protein is already centered).<br>
<br>
After doing this :<br>
<br>
Reading..... <br>
Scaling lipids.... <br>
There are 512 lipids... <br>
with 14 atoms per lipid.. <br>
<br>
Determining upper and lower leaflet...<br>
240 lipids in the upper... 272 lipids in the lower leaflet <br>
</blockquote>
<br></div>
Why are the lipids distributed asymmetrically?<div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Centering protein....<br>
Checking for overlap....<br>
...this might actually take a while....<br>
100 % done... There are 0 lipids within cut-off range...<br>
0 will be removed from the upper leaflet...<br>
0 will be removed from the lower leaflet...<br>
<br>
Writing scaled bilayer & centered protein...<br>
<br>
<br>
Calculating Area per lipid...<br>
Protein X-min/max: 0 133<br>
Protein Y-min/max: 0 133<br>
X-range: 133 A Y-range: 133 A<br>
Building 133 X 133 2D grid on protein coordinates...<br>
Calculating area occupied by protein..<br>
full TMD..<br>
upper TMD....<br>
lower TMD....<br>
Area per protein: 115 nm^2<br>
Area per lipid: 10.6034139525 nm^2<br>
<br>
Area per protein, upper half: 82 nm^2<br>
Area per lipid, upper leaflet : 11.447808216 nm^2<br>
<br>
Area per protein, lower half: 69.25 nm^2<br>
Area per lipid, lower leaflet : 10.1478822494118 nm^2<br>
<br>
Writing Area per lipid...<br>
Done!<br>
<br>
This shows that there are no clashes between lipid and protein but when <br>
</blockquote>
<br></div></div>
What cutoff are you using on the InflateGRO command line? If you are using the default of 14, the particles might be outside of the cutoff, but due to the implied larger size of the coarse particles, the interactions may still be significant at this distance. Try a larger cutoff.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I run EM after this step it gives me lots of lincs warning and errors. I don't know why is that happening and I am using em.mdp file provided by MARTINI because I am working on Coarse Grained. Please help me out if what changes do I need to make to get rid off LINCS.<br>
<br>
</blockquote>
<br></div>
Does the protein minimize by itself? What about the lipids? Where are the LINCS warnings originating? That's the first place to look for the cause of the problems.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks,<br>
<br>
Sunny<br>
<br>
<br>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<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>
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