Justin,<br><br><div class="gmail_quote"><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"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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As I said before, I cannot obtain files from this site.</blockquote><div><br>Could you provide me with the fileshare server wich you have access? I cant uploat files to that mail list indirectly due to the limitation of the size for attached files </div>
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If water is leaking into your membrane, you may have voids between the lipids indicating insufficient packing.
I'm willing to bet that there are some voids somewhere in the simulation box at the outset of the simulation, likely due to the use of an increased vdW radius for carbon. The solvent will fill in the voids over time and the box will change accordingly.</blockquote>
<div><br>It's intresting that water leaking was detected after NPT equilibration exactly. ( after solvating and NVT there are no water molecles inside the membrane ) . Also I've checked how the temperature, pressure and XYZ bondaries of the box have being stabilized and there were not any deviation from the results presented in the tutorial.<br>
<br><br>Also I've tried to prepare same system with the G_membed. Firstly there were removed 4 lipids in comparison to perl program wich removed only 2 lipids. Finally a fter minimisation of that system there already has been some water inside the membrane. By the way I'll try to equilibrate this system and examine results.<br>
<br><br>James</div></div>