Thanks Justin<br><br>I'll try to do that things.<br><br>Some addition questions<br><br>1) About nvt and apt equilibration<br><br>As I understood ref_t of the system must be equal to temperature of the phase transition of the specific LIPID.<br>
But in the npt and nvt.mdp files there are severl enties for ref_t ( for some system groups in index.ndx ) <br>For my system composed of protein dmpc and water :<br><br> ref_t = 323 297 323 ; <br><br>
Does all this values in mdp file must be equal ( to the temperature of the lipid phase transition)<br> ref_t = 297 297 297<br> <br> or each value must correspond to the temperature of phase transition of the individual element ?<br>
ref_t = 323 297 323 ; <br><br>Does thic correct for both NPT and NVT ensembles ?<br><br><br>James<br><br><div class="gmail_quote">2011/11/11 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;"><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;">
Justin,<br>
<br>
Could you tell me what difference in inflategro parameters ( cut-off for lipid removing and scaling factors) should I make for insertion protein in another bilayes in comparison tu tutorial ?<br>
<br>
</blockquote>
<br></div>
I've never made any changes; it's always worked just fine.<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;">
Now I'm working with DMPC. I've inserted symmetrical alpha helices protein in this bilayer but inflategro deleate 2 lipid from upper and just 1 from lower layer. It's strange because I suppose that equal bilayer molecules would be removed :o<br>
<br>
</blockquote>
<br></div>
The number of lipids that are removed will depend on the starting configuration of the membrane and thus where lipids are relative to the protein. Theoretically, a symmetrical protein should delete an equal number of lipids from each leaflet, if the geometry of the top and bottom leaflets is comparable. Either try placing the protein at a different location to achieve equivalent removal or manually delete a lipid and be sure to equilibrate adequately.<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>
On Inflategro's sites I havenot found such specifity for above parameters for different bilayers :(<br>
</blockquote>
<br></div>
The cutoffs specified are simple grid search parameters. They do not necessarily need to be altered depending upon the lipid type.<div><div></div><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>
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