[gmx-users] 4. Requesting advice on pressure scaling in a protein-in-membrane system. (Daniel Adriano Silva M)

[Gerrit Groenhof]

Can you simulate the membrane and protein seperately, thus the two system you are trying to merge?

Gerrit

> 
>  4. Requesting advice on pressure scaling in a
>     protein-in-membrane system. (Daniel Adriano Silva M)
> 


> 
> Dear gmx users and developers,
> 
> I am facing a problem that is new for me and I will appreciate advice from
> your expertise. I am working with a big protein complex (around 100K atoms,
> several subunits) and I used g_membed to embed it in a (aprox 24 14 nm)
> pre-equilibrated POPC membrane, however after embedding and a 1ns of NVT
> equilibration I tried to proced to the NPT equilibration, but I found my
> system exploding (things moving to fast), so I tried several methods that
> came to my mind (like decrease the P-coupling constant, decrease the
> timestep and some others). After few tries I went back to the
> NVT  equilibration and took a look to the pressure, for my surprise I found
> it to be around 1e30! So I ended with a very compressed system on X-Y, I
> guess given the embedding of the protein in the membrane. Here are the
> questions:
> 
> 1) Are there any reasonable simple method to reduce the pressure on the
> protein/lipid system?
> 2) May I expect a very long time to reach the adequate pressure and
> equilibrium given a possible change on the phase of the lipids by the high
> pressure?
> 3) Any other useful direction?
> 
> Extra information: On this step I had frozen the Protein and excluded the
> Protein-Protein energy.
> 
> Thanks,
> Daniel Silva
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> ------------------------------
> 
> Message: 5
> Date: Fri, 07 Jan 2011 10:07:27 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Requesting advice on pressure scaling in	a
> 	protein-in-membrane system.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D272C2F.2070903 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
> Daniel Adriano Silva M wrote:
>> Dear gmx users and developers,
>> 
>> I am facing a problem that is new for me and I will appreciate advice 
>> from your expertise. I am working with a big protein complex (around 
>> 100K atoms, several subunits) and I used g_membed to embed it in a 
>> (aprox 24 14 nm) pre-equilibrated POPC membrane, however after embedding 
>> and a 1ns of NVT equilibration I tried to proced to the NPT 
>> equilibration, but I found my system exploding (things moving to fast), 
>> so I tried several methods that came to my mind (like decrease the 
>> P-coupling constant, decrease the timestep and some others). After few 
>> tries I went back to the NVT  equilibration and took a look to the 
>> pressure, for my surprise I found it to be around 1e30! So I ended with 
>> a very compressed system on X-Y, I guess given the embedding of the 
>> protein in the membrane. Here are the questions:
>> 
>> 1) Are there any reasonable simple method to reduce the pressure on the 
>> protein/lipid system?
>> 2) May I expect a very long time to reach the adequate pressure and 
>> equilibrium given a possible change on the phase of the lipids by the 
>> high pressure?
>> 3) Any other useful direction?
>> 
>> Extra information: On this step I had frozen the Protein and excluded 
>> the Protein-Protein energy.
>> 
> 
> During NVT?  Turn off this freezing before proceeding, doing additional NVT if 
> necessary.  Frozen groups can do weird things, and I would suspect that your 
> system simply isn't stable in the presence of these frozen groups.
> 
> I have a procedure (and troubleshooting tips) for equilibrating membrane protein 
> systems in my tutorial:
> 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
> 
> You may find it useful.  Membrane systems do take a while to converge, but 
> that's not your issue here.  You have some fundamental instability to deal with 
> first.
> 
> -Justin
> 
>> Thanks,
>> Daniel Silva
>> 
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
>