[gmx-users] RE: Energy Minimization - not getting correct lipid area

Sat Jun 9 00:33:43 CEST 2012

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...
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...
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..
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....
Erica

________________________________
From: Justin A. Lemkul [via GROMACS] [ml-node+s5086n4998244h83 at n6.nabble.com]
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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