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

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.
Before inserting the protein the bilayer was alright as I took the
equilibrated bilayer from Dr. Tieleman's website.
I have done the position restraint mdrun by restraining the protein only. In
this case also the lipids pull apart.

Thanking you,
Pawan

On Mon, Apr 6, 2009 at 1:33 PM, Kukol, Andreas <a.kukol at herts.ac.uk> wrote:

> 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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