[gmx-users] Bilayer thickness error
Justin Lemkul
jalemkul at vt.edu
Fri Oct 18 13:38:37 CEST 2013
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
--
==================================================
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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