[gmx-users] Splitted DMPC bilayer

[Justin A. Lemkul]

Dr. Ramón Garduño-Juárez wrote:
> Dear all,
> Dear Justin,
> 
> This time I want to ask the gurus about this problem I encountered in 
> the Equilibration step of my system made of 3 individual (small) protein 
> chains in a solvated DMPC bilayer, no ions present since the protein 
> system is neutral...
> 
> Following the tutorial I started with
> 
>  make_ndx_d -f em_after_solv.gro -o index_after_solv.ndx
> 
> for which I got the following list:
> -----------------------------------------------------------------
> Reading structure file
> Going to read 0 old index file(s)
> Analysing residue names:
> There are:   129    Protein residues
> There are:   123      Other residues
> There are:  3215      Water residues
> Analysing Protein...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting 
> into groups...
> 
>   0 System              : 16649 atoms
>   1 Protein             :  1346 atoms
>   2 Protein-H           :  1025 atoms
>   3 C-alpha             :   129 atoms
>   4 Backbone            :   387 atoms
>   5 MainChain           :   519 atoms
>   6 MainChain+Cb        :   636 atoms
>   7 MainChain+H         :   649 atoms
>   8 SideChain           :   697 atoms
>   9 SideChain-H         :   506 atoms
>  10 Prot-Masses         :  1346 atoms
>  11 non-Protein         : 15303 atoms
>  12 Other               :  5658 atoms
>  13 DMPC                :  5658 atoms
>  14 Water               :  9645 atoms
>  15 SOL                 :  9645 atoms
>  16 non-Water           :  7004 atoms
> -----------------------------------------------------
> 
> Since I did not add ions I have formed a (merged) group named SOL_SOL 

Why would you merge solvent with itself?

> after chosing  15 | 15 , and another merged group named Protein_DMPC by 
> choosing  1 | 13...
> 
> Next, I started the NVT equilibration with:
> 
> grompp_d  -f nvt.mdp  -c em_after_solv.gro  -p topol_mod_lip_solv.top  
> -n index_after_solv.ndx  -o nvt.tpr
> 
> The nvt.mpd file is the same as the one given in the tutorial, the only 
> changes I made were:
> 
> tc-grps            = Protein DMPC SOL_SOL
> and
> comm-grps    = Protein_DMPC SOL_SOL
> 

I would think that using this weird SOL_SOL group would create problems related 
to degrees of freedom, etc.  If you have no ions, there is no need to merge any 
sort of solvent-related groups.

> After this I ran
> 
> mdrun_mpi_d  -v  -deffnm nvt
> 
> When this process is finished I looked at the resulting nvt.gro file and 
> found the following:
> 
> 1) The 3 protein chains complex is fine, at the center of the box as it 
> should be, but
> 2) The 2 DMPC layer are separated (splitted) leaving a large gap between 
> them forming a )( shape where the top and bottom of this figure contain 
> one layer of DMPC plus water molecules, while in the narrow section the 
> protein complex is found... In the void between the two DMPC layers no 
> water molecules are present...  Very odd!...
> 
> Please advice...
> 

This is covered in the "Advanced Troubleshooting" section of my tutorial:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/advanced_troubleshooting.html

-Justin

> Cheers,
> Ramon Garduno
> 

-- 
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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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