Respected Sir,<br><br>Greetings from Pawan.<br>Before inserting the protein the bilayer was alright as I took the equilibrated bilayer from Dr. Tieleman's website.<br>I have done the position restraint mdrun by restraining the protein only. In this case also the lipids pull apart.<br>
<br>Thanking you,<br>Pawan<br><br><div class="gmail_quote">On Mon, Apr 6, 2009 at 1:33 PM, Kukol, Andreas <span dir="ltr"><<a href="mailto:a.kukol@herts.ac.uk">a.kukol@herts.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
There is nothing wrong with the number of steps and the step size of 2 fs. Can you attach/send the coordinates of your system after position restraint MD ?<br>
<br>
What about your bilayer before inserting the protein ? Does it move apart during MD ?<br>
<br>
Definetly you should perform another position restraint MD, restraining the protein only.<br>
<div class="im"><br>
Andreas<br>
<br>
>>>>>>>>>>>>>>>><br>
From: <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>] On Behalf Of Pawan Kumar<br>
</div>Sent: 06 April 2009 08:51<br>
<div class="im">To: Discussion list for GROMACS users<br>
</div><div><div></div><div class="h5">Subject: [gmx-users] Doubt regarding membrane protein in POPC bilayer<br>
<br>
Respected Sir,<br>
<br>
Greetings from Pawan.<br>
Thanks for your reply.<br>
After the position restraint mdrun the system looked quite justified as I restrained both the protein and the lipids.<br>
Is it because of the lesser number of steps ? I use 5000 steps with dt value of 0.002.<br>
<br>
Thanking you,<br>
Pawan<br>
On Mon, Apr 6, 2009 at 1:11 PM, Kukol, Andreas <<a href="mailto:a.kukol@herts.ac.uk">a.kukol@herts.ac.uk</a>> wrote:<br>
Apparently the final mdrun has not worked successfully. It would be interesting to see what the system looks like after the position restraint mdrun.<br>
<br>
Andreas<br>
<br>
>>>>>>>>>>><br>
From: <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>] On Behalf Of Pawan Kumar<br>
Sent: 06 April 2009 07:47<br>
To: Discussion list for GROMACS users; <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a><br>
Subject: [gmx-users] Doubt regarding membrane protein in POPC bilayer<br>
<br>
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>
On Tue, Mar 31, 2009 at 5:50 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
<br>
<br>
Pawan Kumar wrote:<br>
Respected Sir,<br>
<br>
Greetings from Pawan.<br>
Thanks for all your kind help and suggestions.<br>
I will work on this and ask you if I have further doubts.<br>
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>
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>
Thanking you,<br>
<br>
Yours sincerely,<br>
Pawan<br>
--<br>
========================================<br>
<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>
<br>
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