[gmx-users] EM with inflategro

[Justin A. Lemkul]

sunny mishra wrote:
> I did the catting of lipid.gro and protein.gro and named it as 
> system.gro and then I inflated DSPC using INFLATEGRO script command and 
> also I am using the default value of 14A for cut off distance. So I 
> don't have much idea that after inflating the whole system if I run the 
> EM then protein and lipid should minimize.
> 

This information doesn't answer my questions.  Think scientifically - your 
system is unstable.  What are the possible sources?  The protein model is poor, 
the lipid structure is poorly optimized, or there is a clash between the protein 
and lipid.  You can systematically eliminate each one if you minimize each 
component separately before constructing the system.

> LINCS warning originates from the very first step as I my stepsize is 
> 1000 and dt=.03 (provided by MARTINI) and LINCS says that there are 22 
> inconsistent shifts and the maximum force is at atom 3373 which is 
> 8.153704e+04. Do you have any idea?
> 

Are you sure you're running EM?  If so, then dt doesn't matter.  If your 
stepsize is 1000, that is certainly wrong.

-Justin

> Sunny
> 
> On Mon, Nov 2, 2009 at 4:49 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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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

========================================