Respected Sir,<br><br>Greetings from Pawan.<br>Thanks for all your suggestions and help.<br>The solvation is completed and the system is neutralized.<br>The position restraint mdrun and final mdrun has worked out successfully without any warnings and errors this time.<br>
The structure after the final mdrun is not quite acceptable as the lipids have pulled apart and there is a huge gap between the two layers of the lipids. I have made the run for 5000 steps with dt = 0.002.<br>Any suggestions please.<br>
<br>Thanking you,<br><br>Yours sincerely,<br>Pawan<br><br><div class="gmail_quote"><div class="im">On Tue, Mar 31, 2009 at 5:50 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
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<br>
Pawan Kumar wrote:<br>
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Respected Sir,<br>
<br>
Greetings from Pawan.<br></div><div>
Thanks for all your kind help and suggestions.<br>
I will work on this and ask you if I have further doubts.<br></div>
Is it fine if I use the perl code given in <a href="http://wiki.gromacs.org/membrane-simulations" target="_blank">wiki.gromacs.org/membrane-simulations</a> <<a href="http://wiki.gromacs.org/membrane-simulations" target="_blank">http://wiki.gromacs.org/membrane-simulations</a>> for solvation after the genbox step to remove extra waters from the hydrophobic part of the bilayer ?<br>
<br>
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<br>
You mean the C program or shell script at <a href="http://wiki.gromacs.org/index.php/Membrane_Simulations" target="_blank">http://wiki.gromacs.org/index.php/Membrane_Simulations</a>? Yes, either of those should be fine.<br>
<br>
-Justin<br>
<br>
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Thanking you,<br>
<br>
Yours sincerely,<br>
Pawan<br>
<br></div><div class="im">
-- <br>
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<br>
Justin A. Lemkul<br>
Graduate Research Assistant<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>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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