[gmx-users] EM in kalp15_DPPC
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
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..
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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