[gmx-users] EM with inflategro
mishra.sunny at gmail.com
Mon Nov 2 23:15:44 CET 2009
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
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?
On Mon, Nov 2, 2009 at 4:49 PM, Justin A. Lemkul <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 :
>> 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
>> 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...
>> 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.
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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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
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