[gmx-users] Maximum force on atom and unpacked lipids

sdshine sdshine at gmail.com
Tue Apr 2 11:56:48 CEST 2013

Dear Users,

I have inserted protein and carbohydrate in DPPC membrane according to the
tutorials. After inserting both molecules, I checked by using VMD, the atoms
around my protein and ligand were overlapped. But I applied position
restraints to protein and ligand and  run 
Inflategro scripts for shrinking and packing.

Perl inflategro result
There are 3 lipids within cut-off range...
1 will be removed from the upper leaflet...
2 will be removed from the lower leaflet...
Writing scaled bilayer & centered protein...

Calculating Area per lipid...
Protein X-min/max: 11    47
Protein Y-min/max: 19    45
X-range: 36 A    Y-range: 26 A
Building 36 X 26 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD....
lower TMD....
Area per protein: 7.5 nm^2
Area per lipid: 10.4673818624 nm^2

Area per protein, upper half: 5.5 nm^2
Area per lipid, upper leaflet : 10.4160534349206 nm^2

Area per protein, lower half: 4.25 nm^2
Area per lipid, lower leaflet : 10.6042155870968 nm^2

Writing Area per lipid...

1st EM result
Step=  576, Dmax= 8.0e-03 nm, Epot= -9.29249e+04 Fmax= 5.95606e+03, atom=
Step=  578, Dmax= 4.8e-03 nm, Epot= -9.29638e+04 Fmax= 8.42117e+02, atom=

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1000 in 579 steps
Potential Energy  = -9.2963797e+04
Maximum force     =  8.4211664e+02 on atom 504
Norm of force     =  4.9797871e+01

Then in EM step, showing Maximum force on certain atom.
I performed shrinking step until it converged. But every EM I have Max Force
on selected atom.
The final complex still have unpacked lipids.
How to correct this or whether will be corrected during Equilibration steps.
I think the problem lies in the Ist EM step itself. 
Kindly give some suggestions

Thanks in advance

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