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.
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? Sunny On Mon, Nov 2, 2009 at 4:49 PM, Justin A. Lemkul <[email protected]> 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 >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > 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 > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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