[gmx-users] POPC Membrane + protein dynamics

[Justin A. Lemkul]

padhu at ncbs.res.in wrote:
> Dear All,
> I'm a new comer to gromacs. I need to perform molecular dynamics
> simulation of my protein within the POPC membrane. I have downloaded the
> 128a popc lipid from Prof.Tieleman's group along with the required
> popc.itp. My protein of interest is 458 residues. Since the 128a popc is
> already Simulated for 1600 ps, i haven't done membrane only simulation. So
> i directly aligned my protein with the membrane using VMD and have saved
> the coordinates. However after i aligned my protein with the membrane, i
> felt the membrane was not big enough for my protein of interest, also, the
> N-terminal region and the loop regions in the C-terminal region and
> stretching outside water molecule above and below respectively.ow, i have
> two questions here...

Yep, if the protein is sticking "out" of the box on both sides, the box is too 
small.

> 1. How would i increase the number of lipids from the existing one?

Two options:

1. genconf -nbox will give integer multiples of the lipid system (i.e., -nbox 2 
2 1 will expand the bilayer in the x and y directions and give 512 lipids)

2. genbox -cs popc128a.pdb -box (whatever dimensions) allows you a bit finer 
control over how large the box is and how many lipids will result.

> 2. Also, i should increase increase the number of water molecules above
> and below the membrane so that it covers the whole region of N-terminal
> and also the loop regions of the C-terminal.

Expand the box using editconf and add solvent with genbox.

> Now, How to perform these tasks??If i do so will it be compatible with the
> popc.itp file which i downloaded from the Prof. Tieleman's group?
> 

None of the above operations have any influence on the parameters contained in 
popc.itp.  If you are unsure about Gromacs workflows, file formats, etc. then 
you really need read the manual and do some more basic tutorial material before 
you attempt a difficult simulation like a membrane protein.  There are a lot of 
pitfalls in simulating such a complex system, and if you are not ready for them, 
then you can waste a whole lot of time generating nonsensical results :)

> 3. My third question is while aligning my protein with the membrane should
> i make a hole first or after aligning the protein should i remove the
> overlapping lipids with the proteins?which one would be better??
> 

There are several methods for doing this.  See below.

> I have tried out some of the methodologies available in the internet but
> it dosen't help me.If anyone of you have a detailed step by step
> methodology right from the first step to till running the MD simulation
> please let me know.

Saying you've tried things and they didn't work is useless.  What did you try? 
What links can you provide?  Have you tried the membrane protein tutorial linked 
from the Gromacs site?  That's about as step-by-step as it gets.

-Justin

> Your help will be highly appreciated.
> Looking forward to hear from you.
> 
> Best regards
> Padmanabhan
> 

-- 
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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

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