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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists