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

[Justin A. Lemkul]

Pawan Kumar wrote:
> 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.
> 

There are several possibilities for why this is may be happening.

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.
2. 5000 steps is far too short to expect any realistic behavior for lipids. 
Equilibration can take upwards of 10-20 ns.
3. You haven't mentioned the contents of your .mdp file.  Maybe you're doing 
something wrong.
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.

-Justin

> Thanking you,
> 
> Yours sincerely,
> Pawan
> 
> On Tue, Mar 31, 2009 at 5:50 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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>
>         <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 <http://vt.edu/> | (540) 231-9080
>         http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>         ========================================
> 
> 
> 

-- 
========================================

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

========================================