[gmx-users] EM with inflategro

sunny mishra mishra.sunny at gmail.com
Mon Nov 2 22:40:32 CET 2009


Hi All,

I am having a trouble during EM step after I inflategro my lipid.gro
(protein is already centered).

After doing this :

Reading.....

Scaling
lipids....

There are 512
lipids...

with 14 atoms per
lipid..


Determining upper and lower leaflet...
240 lipids in the upper...
272 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: 0    133
Protein Y-min/max: 0    133
X-range: 133 A    Y-range: 133 A
Building 133 X 133 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD....
lower TMD....
Area per protein: 115 nm^2
Area per lipid: 10.6034139525 nm^2

Area per protein, upper half: 82 nm^2
Area per lipid, upper leaflet : 11.447808216 nm^2

Area per protein, lower half: 69.25 nm^2
Area per lipid, lower leaflet : 10.1478822494118 nm^2

Writing Area per lipid...
Done!

This shows that there are no clashes between lipid and protein but when I
run EM after this step it gives me lots of lincs warning and errors. I don't
know why is that happening and I am using em.mdp file provided by MARTINI
because I am working on Coarse Grained. Please help me out if what changes
do I need to make to get rid off LINCS.

Thanks,

Sunny
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