[gmx-users] Bilayer thickness error

[Justin Lemkul]

On 10/18/13 2:54 AM, Archana Sonawani-Jagtap wrote:
> Hi,
> This is my input file for calculating bilayer thickness in absence of peptide:
> ###### Input file and input file parameters
> 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                solvent
> grid                        20
> conserve_ratio        yes
> ###### Define whether there is a protein embedded in the bilayer
> protein                   no
> precision               1.3
> P_value                 5.0
> ###### Define the desired output files and format
> output_prefix           output
> output_format          column
> thickness                   yes
> area                           no
>
> I got 400 lines in one column in output file for average thickness
> (calculated without peptide)
>
> When running in Gnuplot I get following error:
> splot 'output.frame1.20x20.average_thickness.dat' matrix using (1+$1):(1+$2):3
> Warning: empty x range [1:1], adjusting to [0.99:1.01]
>

Please refer to Appendix A, section 2 of our GridMAT-MD manual, which explains 
the preprocessing necessary to open the file in Gnuplot, otherwise refer to the 
manual section describing the output_format keyword.

You can send GridMAT-MD questions directly to me; there is no need to fill 
peoples' inboxes with non-Gromacs questions.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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