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
