[gmx-users] EM with inflategro

[Justin A. Lemkul]

sunny mishra wrote:
> 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      
> 

Why are the lipids distributed asymmetrically?

> 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 

What cutoff are you using on the InflateGRO command line?  If you are using the 
default of 14, the particles might be outside of the cutoff, but due to the 
implied larger size of the coarse particles, the interactions may still be 
significant at this distance.  Try a larger cutoff.

> 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.
> 

Does the protein minimize by itself?  What about the lipids?  Where are the 
LINCS warnings originating?  That's the first place to look for the cause of the 
problems.

-Justin

> Thanks,
> 
> Sunny
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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