[gmx-users] (no subject)

[Archana Sonawani-Jagtap]

Hi,

Please tell me what is wrong in my input file. I am not getting APL
along with std deviation values.

Following is the input and output for calculating APL
Input file
coord_file              md.gro
file_type                   gro
num_frames                1
num_lipid_types         1
resname1                  POPC
atomname1               P8
solvent                     SOL
ions                          CL-
###### Define the size and shape of the grid
box_size                vectors
grid                    200
conserve_ratio          yes
###### Define whether there is a protein embedded in the bilayer
protein                 yes
precision               1.3
P_value                 6.0
###### Define the desired output files and format
output_prefix           output
output_format           column
thickness               no
area                    yes

Output:
Reading from "PC_APL"...
You defined the coordinate file as md.gro
You specified that this file contains 1 frame(s)
You defined a lipid residue name as POPC (atom(s): P8)
You defined the solvent as SOL
You defined the ions as CL-

Deconstructing lipid bilayer...
Lower X limit: 0.436599999999999   Upper X limit: 6.696
Lower Y limit: 0.2762   Upper Y limit: 6.476
Cross sectional area (box size) was determined from: a line in the coord file
Cross sectional area of the system: 6.25940 x 6.19980 nanometers
Lower Z limit: -0.328   Upper Z limit: 5.269
The middle (in the Z-direction) is 2.4705
In the top leaflet, the Z values range from 4.223 to 5.269
In the bottom leaflet, the Z values range from -0.328 to 1.616

Simulating periodic boundary conditions...Done
Dividing the periodic array into a top and bottom leaflet...Done

Looking for offending protein atoms...
There are 10 protein atoms within the headgroups of the top leaflet
There are 18 protein atoms within the headgroups of the bottom leaflet

Simulating periodic boundary conditions for the protein atoms...Done
Dividing the periodic array into a top and bottom leaflet...Done

Generating the grid...
Your system is bigger in the X-direction
There are 200 grid points in the X direction, spaced every 0.03145 nanometers
There are 198 grid points in the Y direction, spaced every 0.03147 nanometers
Note: the intervals may not be exactly the same in order to have a
whole number of grid points

Analyzing the bilayer...

Calculating area per lipid head group...
The lateral area of the system is 3880.70281 sq. Angstroms (per side)
When you don't account for any protein atoms:
    The average area per lipid in the top leaflet is 61.59846 sq. Angstroms
    The average area per lipid in the bottom leaflet is 59.70312 sq. Angstroms
When you do take the protein atoms into account:
    The new area per lipid in the top leaflet is 60.66670 sq. Angstroms
    The new area per lipid in the bottom leaflet is 54.70072 sq. Angstroms
The top leaflet lipid areas will be printed to
output.frame1.200x198.top_areas.d at
The bottom leaflet lipid areas will be printed to
output.frame1.200x198.bottom_a reas.dat

-- 
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339