Justin,<br><br><br>Indeed GenBox added insufficien of the SOL to my system due to the ussage of increased vdvdat ( I've used 0.350 value for the c atoms only but the were alot of void beetwen water and bilayer )<br><br>
lipid_posres in Z directions have prevented the displacement of the bilayer but the water were distruibuted irregular on the bilayer surface at the end of NVT phase<br><br>By the way in Gmembed system I have no such problems because the were no need to use genbox but during processing of the system I've obtain warning<br>
<br><pre>WARNING 1 [file membed.mdp]:<br> Can not exclude the lattice Coulomb energy between energy groups</pre>
<br><br>What does it mean?<br><br>By the way could I indicate Area per lipid during processing of my system with the G_membed?<br><br><br>James<br><br><pre><br></pre><br><br><div class="gmail_quote">2011/11/11 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">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><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>
The system was compact after inserting protein into bilayer (I've obtain Area per lipid in accordanc with experimental reference) and futher minimization (only some llipid tails on the border of the system were distorded alittle)<br>
But after nvt simulation this discrepancy occured :)<br>
<br>
I've used pbc size like in the KALP simulation because I have bilayer ( 128 lipids) and the protein (38 a.a) of the same size.<br>
</blockquote>
<br></div>
KALP-15 has only 15 residues; your peptide is significantly longer.<div><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
My box vectors were 6.500 6.500 6.500<br>
<br>
Do you think that I should use smaller pbc? How I could define pbc on the right size for my purely bilayer system?<br>
<br>
</blockquote>
<br></div>
You shouldn't use the box vectors I did in the tutorial - use the dimensions present in the actual membrane you're using. I still see no conceivable way that the bilayer separated that much during NVT without significant empty space in the unit cell to start. In NVT, the volume is constant, so if there are voids, the lipids will fill to expand them. I've seen it countless times, so please be sure you're actually providing sufficient solvent and an appropriate location for all your components within the unit cell.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div>
I've used<br>
<br>
trjconv -s em.tpr -f dmpc128.gro -o dmpc128_whole.gro -pbc mol -ur compact<br>
<br>
at the preequilibrated bilayer and than done anything in accordance to the KALP tutorial<br>
<br>
<br>
James<br>
<br>
<br></div>
2011/11/11 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><div><br>
<br>
How large of a void exists between your lipids and water prior to<br>
starting the simulation? I'm almost certain that you built the unit<br>
cell incorrectly - there should never be that much free space.<br>
<br>
<br>
<br>
By the way I'ts intresting that Gmembed has removed 6 lipids in<br>
comparison to the inflateglo ( althought I've done all things in<br>
accordance to the KALP tutorial because my protein is the same).<br>
<br>
<br>
Different algorithms, different results. Nothing odd about that to me.<br>
<br>
-Justin<br>
<br>
<br></div>
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Justin A. Lemkul<br>
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Virginia Tech<br>
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