[gmx-users] Splitted DMPC bilayer

"Dr. Ramón Garduño-Juárez" ramon at fis.unam.mx
Wed Mar 30 20:22:09 CEST 2011

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 
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
comm-grps    = Protein_DMPC SOL_SOL

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...

Ramon Garduno
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