From: Justin A. Lemkul [via GROMACS]
[[email protected]] Sent: Friday, June 08, 2012 5:42 PM
To: Hicks, Erica Subject: RE: Energy Minimization - not getting correct lipid
area
On 6/8/12 6:33 PM, Erica Hicks wrote:
Hi,
bash-3.2$ perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5
area.dat Reading..... Scaling lipids.... There are 128 lipids... with 50
atoms per lipid..
Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids
in the lower leaflet
Centering protein.... Checking for overlap.... ...this might actually take
a while.... 100 % done... There are 2 lipids within cut-off range... 1 will
be removed from the upper leaflet... 1 will be removed from the lower
leaflet...
Writing scaled bilayer& centered protein...
Calculating Area per lipid... Protein X-min/max: 26 40 Protein
Y-min/max: 25 39 X-range: 14 A Y-range: 14 A Building 14 X 14 2D grid
on protein coordinates... Calculating area occupied by protein.. full
TMD.. upper TMD.... lower TMD.... Area per protein: 2 nm^2 Area per lipid:
10.4716089904762 nm^2
Area per protein, upper half: 1.75 nm^2 Area per lipid, upper leaflet :
10.4755772444444 nm^2
Area per protein, lower half: 2 nm^2 Area per lipid, lower leaflet :
10.4716089904762 nm^2
Writing Area per lipid... Done!
bash-3.2$ mdrun -v -deffnm em Back Off! I just backed up em.log to
./#em.log.6# Getting Loaded... Reading file em.tpr, VERSION 4.5.4 (single
precision) Starting 4 threads Loaded with Money
Making 1D domain decomposition 4 x 1 x 1
Back Off! I just backed up em.trr to ./#em.trr.6#
Back Off! I just backed up em.edr to ./#em.edr.6#
Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps =
50000 Step= 0, Dmax= 1.0e-02 nm, Epot= -3.06212e+05 Fmax= 5.37269e+03,
atom= 3275 Step= 1, Dmax= 1.0e-02 nm, Epot= -3.10498e+05 Fmax=
2.40668e+03, atom= 3024 Step= 3, Dmax= 6.0e-03 nm, Epot= -3.10958e+05
Fmax= 2.89119e+03, atom= 4225 Step= 5, Dmax= 3.6e-03 nm, Epot=
-3.12589e+05 Fmax= 1.46767e+03, atom= 1365 Step= 6, Dmax= 4.3e-03 nm,
Epot= -3.13033e+05 Fmax= 3.83969e+03, atom= 1365 Step= 7, Dmax= 5.2e-03
nm, Epot= -3.13599e+05 Fmax= 2.88720e+03, atom= 1365 Step= 8, Dmax=
6.2e-03 nm, Epot= -3.13688e+05 Fmax= 4.93154e+03, atom= 1365 Step= 9,
Dmax= 7.5e-03 nm, Epot= -3.14101e+05 Fmax= 4.72541e+03, atom= 1365 Step=
11, Dmax= 4.5e-03 nm, Epot= -3.14800e+05 Fmax= 9.90227e+02, atom= 1365
writing lowest energy coordinates.
Back Off! I just backed up em.gro to ./#em.gro.6#
Steepest Descents converged to Fmax< 1000 in 12 steps Potential Energy =
-3.1480012e+05 Maximum force = 9.9022711e+02 on atom 1365 Norm of
force = 1.2180042e+02
bash-3.2$ perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink1.gro 5
area_shrink1.dat Reading..... Scaling lipids.... There are 128 lipids...
Something is wrong here. You should only have 126 lipids since 2 were
removed before. Did you minimize the correct coordinate file?
with 50 atoms per lipid..
Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids
in the lower leaflet
No protein coordinates found...
This is also strange. This, coupled with the lines above regarding the
number of lipids, suggest you're using the wrong coordinate file.
Writing scaled bilayer& centered protein...
Calculating Area per lipid... Protein X-min/max: 10000 -9999 Protein
Y-min/max: 10000 -9999 X-range: -19999 A Y-range: -19999 A Building
-19999 X -19999 2D grid on protein coordinates... Calculating area occupied
by protein.. full TMD.. upper TMD.. lower TMD..
The following areas are meaningless, for reasons associated with incorrect
content or processing thereof.
Area per protein: 0 nm^2 Area per lipid: 0.583197761890625 nm^2
Area per protein, upper half: 0 nm^2 Area per lipid, upper leaflet :
0.583197761890625 nm^2
Area per protein, lower half: 0 nm^2 Area per lipid, lower leaflet :
0.583197761890625 nm^2
Writing Area per lipid... Done!
To me, it looks like it is not looking at the 126 lipids that I updated in
the topology file. Hmmmm....
OK, I seem to remember 124 being what my system produced, but that's
irrelevant. Check out the lines above.
Erica
________________________________ From: Justin A. Lemkul [via GROMACS]
[[hidden email]<UrlBlockedError.aspx>] Sent: Friday, June 08, 2012 5:21 PM
To: Hicks, Erica Subject: RE: Energy Minimization - not getting correct
lipid area
On 6/8/12 6:18 PM, Erica Hicks wrote:
Hi,
Everything should be updated correctly. I added in the DPPC 128
underneath the protein in [molecules] but I still get the same results.
What do you mean by " Further manual modifications are necessary based on
how many lipids InflateGRO removes"? After I generated the new position
restrain file, I updated the minim.mdp withe the correct info. I then
scaled by a factor of 4, updated [molecules], ran energy minimization
(mdrun -v -deffnm em), and
This is all my comment meant. If InflateGRO removes 4 lipids, then you
have 124 left, which it sounds like you have accounted for.
scaled by a factor 0.95. I have no idea what could possibly going wrong.
Maybe something with the manipulation of InflateGRO????
Please provide the entire screen output of the first shrinking step that
InflateGRO produces.
-Justin
-- ========================================
Justin A. Lemkul, Ph.D. Research Scientist 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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