[gmx-users] EM in kalp15_DPPC

Shima Arasteh shima_arasteh2001 at yahoo.com
Tue Aug 21 12:14:05 CEST 2012


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

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

The EM contains a warning:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000
Warning: 1-4 interaction between 2321 and 2325 at distance 2.307 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

but because of the -maxwarn 1 its output is:

Steepest Descents converged to Fmax < 1000 in 557 steps
Potential Energy  = -9.2383398e+04
Maximum force     =  9.0041455e+02 on atom 65
Norm of force     =  7.1919853e+01

First, is it acceptable to ignore that warning? 

# perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
Determining upper and lower leaflet...
66 lipids in the upper...
62 lipids in the lower leaflet 

Centering protein....
Writing scaled bilayer & centered protein...

Calculating Area per lipid...
Protein X-min/max: 122    136
Protein Y-min/max: 122    135
X-range: 14 A    Y-range: 13 A
Building 14 X 13 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: 9.29991419025 nm^2

Area per protein, upper half: 1.75 nm^2
Area per lipid, upper leaflet : 9.02188648751515 nm^2

Area per protein, lower half: 2 nm^2
Area per lipid, lower leaflet : 9.59991142219355 nm^2

Writing Area per lipid...

Here, the area per lipid is too far from 71 Å2!

Thanks for your suggestions.
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