[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Kukol, Andreas]

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 ?

What about your bilayer before inserting the protein ?  Does it move apart during MD ?

Definetly you should perform another position restraint MD, restraining the protein only.

Andreas

>>>>>>>>>>>>>>>>
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Pawan Kumar
Sent: 06 April 2009 08:51
To: Discussion list for GROMACS users
Subject: [gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Sir,

Greetings from Pawan.
Thanks for your reply.
After the position restraint mdrun the system looked quite justified as I restrained both the protein and the lipids.
Is it because of the lesser number of steps ? I use 5000 steps with dt value of 0.002.

Thanking you,
Pawan
On Mon, Apr 6, 2009 at 1:11 PM, Kukol, Andreas <a.kukol at herts.ac.uk> wrote:
Apparently the final mdrun has not worked successfully. It would be interesting to see what the system looks like after the position restraint mdrun.

Andreas

>>>>>>>>>>>
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Pawan Kumar
Sent: 06 April 2009 07:47
To: Discussion list for GROMACS users; jalemkul at vt.edu
Subject: [gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Sir,

Greetings from Pawan.
Thanks for all your suggestions and help.
The solvation is completed and the system is neutralized.
The position restraint mdrun and final mdrun has worked out successfully without any warnings and errors this time.
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.
Any suggestions please.

Thanking you,

Yours sincerely,
Pawan
On Tue, Mar 31, 2009 at 5:50 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:


Pawan Kumar wrote:
Respected Sir,

Greetings from Pawan.
Thanks for all your kind help and suggestions.
I will work on this and ask you if I have further doubts.
Is it fine if I use the perl code given in wiki.gromacs.org/membrane-simulations <http://wiki.gromacs.org/membrane-simulations> for solvation after the genbox step to remove extra waters from the hydrophobic part of the bilayer ?

You mean the C program or shell script at http://wiki.gromacs.org/index.php/Membrane_Simulations?  Yes, either of those should be fine.

-Justin
Thanking you,

Yours sincerely,
Pawan
--
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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