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