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 <[email protected]
<mailto:[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
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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
========================================
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