[gmx-users] kalp15 in dppc and EM iteration

[Shima Arasteh]

Sorry, please don't care about this email. I made a mistake here.

Thanks
Sincerely,
Shima


________________________________
From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Tuesday, August 21, 2012 12:47 PM
Subject: [gmx-users] kalp15 in dppc and EM iteration

Dear users,

I'm doing the KALP-15 IN DPPC through the Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
The problem I got stuck into is in "2. Pack the lipids around the protein" step
After generating the new position restrain file, I start to energy minimization to get the correct area per lipid. As below:

 Scale the lipid positions by a factor of 4:
     #perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat

 LOOP :
    "
     Energy minimization with restrained protein
     #grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr -maxwarn 1
     #mdrun -deffnm em
     scale down the lipids by a factor of 0.95
     #perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
    "


The outputs of the first repeat are:
#perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat

There are 128 lipids...
with 50 atoms per lipid..

Determining upper and lower leaflet...
65 lipids in the upper...
63 lipids in the lower leaflet 

Centering protein....
Checking for overlap....
...this might actually take a while....
100 % done...
There are 0 lipids within cut-off range...
0 will be removed from the upper leaflet...
0 will be removed from the lower leaflet...

Writing scaled bilayer & centered protein...


Calculating Area per lipid...
Protein X-min/max: 26    40
Protein Y-min/max: 25    39
X-range: 14 A    Y-range: 14 A
Building 14 X 14 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD....
lower TMD....
Area per protein: 2 nm^2
Area per lipid: 10.3079901 nm^2

Area per protein, upper half: 1.75 nm^2
Area per lipid, upper leaflet : 10.1532517907692 nm^2

Area per protein, lower half: 2 nm^2
Area per lipid, lower leaflet : 10.4716089904762 nm^2

Writing Area per lipid...
Done!

#grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr -maxwarn 1
#mdrun -deffnm em

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000
Warning: 1-4 interaction between 2008 and 2013 at distance 2.238 which is larger than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Segmentation fault

# perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
Calculating Area per lipid...
Protein X-min/max: 10000    -9999
Protein Y-min/max: 10000    -9999
X-range: -19999 A    Y-range: -19999 A
Building -19999 X -19999 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD..
lower TMD..
Area per protein: 0 nm^2
Area per lipid: 0.583197761890625 nm^2

Area per protein, upper half: 0 nm^2
Area per lipid, upper leaflet : 0.557084429268657 nm^2

Area per protein, lower half: 0 nm^2
Area per lipid, lower leaflet : 0.611879619032787 nm^2

Writing Area per lipid...
Done!

What's the problem? Any steps done incorrectly?



Thanks for your suggestions.
Sincerely,
Shima 
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