On 8/21/12 6:14 AM, Shima Arasteh wrote:
Hi,
I'm doing the KALP-15 IN DPPC through the Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
The problem I got stuck into, is in "2. Pack the lipids around the protein"
step.
After generating the new position restrain file, I start to energy minimization
to get the correct area per lipid. As below:
Scale the lipid positions by a factor of 4:
#perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
LOOP :
"
Energy minimization with restrained protein
#grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
-maxwarn 1
Why are you using -maxwarn? It's almost always a bad idea. What error are you
trying to circumvent?
#mdrun -deffnm em
scale down the lipids by a factor of 0.95
#perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink1.gro 5
area_shrink1.dat
"
The EM contains a warning:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Warning: 1-4 interaction between 2321 and 2325 at distance 2.307 which is
larger than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
but because of the -maxwarn 1 its output is:
Steepest Descents converged to Fmax < 1000 in 557 steps
Potential Energy = -9.2383398e+04
Maximum force = 9.0041455e+02 on atom 65
Norm of force = 7.1919853e+01
First, is it acceptable to ignore that warning?
Generally not. You should check your input and output configurations carefully.
Something is wrong.
# perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
Determining upper and lower leaflet...
66 lipids in the upper...
62 lipids in the lower leaflet
Centering protein....
Writing scaled bilayer & centered protein...
Calculating Area per lipid...
Protein X-min/max: 122 136
Protein Y-min/max: 122 135
X-range: 14 A Y-range: 13 A
Building 14 X 13 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: 9.29991419025 nm^2
Area per protein, upper half: 1.75 nm^2
Area per lipid, upper leaflet : 9.02188648751515 nm^2
Area per protein, lower half: 2 nm^2
Area per lipid, lower leaflet : 9.59991142219355 nm^2
Writing Area per lipid...
Done!
Here, the area per lipid is too far from 71 Å2!
Then you haven't done enough iterations of shrinking. The outcome from 26
iterations of shrinking is very reproducible.
-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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