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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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