<br><div class="gmail_quote"><div class="im">Respected Sir,<br><br>Greetings from Pawan.<br></div><div class="gmail_quote"><div> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
1. Were there gaps between the water and lipid headgroups? If so, the lipids may be pulling towards the solvent. Restrain the lipids and run an equilibration for a longer time.</blockquote><div>Gap was there when I used a value of 0.5 in the vdwradii.dat file. The gap reduced as I decreased the value from 0.5 to 0.35 to the default of 0.15. I tried all the three possibilities.<br>
When I used the default vdwradii.dat file and made the solvation followed by simulation runs the lipids didnt pull apart. But there were water molecules on the sides of the bilayer and not in the interior.<br></div><div class="im">
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2. 5000 steps is far too short to expect any realistic behavior for lipids. Equilibration can take upwards of 10-20 ns.</blockquote></div><div>As per your suggestion I have made the final mdrun now again with 500000 steps. Hopefully this will work.<br>
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3. You haven't mentioned the contents of your .mdp file. Maybe you're doing something wrong.</blockquote></div><div>I am using the same .mdp file which I posted before. I have just removed the restraints. <br></div>
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4. Are you using Gromos/Berger or OPLS/converted Berger for your system? There have been so many of these questions from different users over the last few days that it's hard to keep track. If you are using OPLS/converted Berger you may have made a mistake in translating the C6/C12 parameters.</blockquote>
</div><div>I am using gromos 96 force field (G43a1) and as per your suggestion I have edited the lipid.itp file to remove the part containing " lipid-gromos interactions".<div class="im"><br><br><br>Thanking you,<br>
<br>Yours sincerely,<br>
Pawan<br></div></div></div><br>
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