[gmx-users] Bilayer thickness error

[Archana Sonawani-Jagtap]

thank you so much. It was such a stupid error from my side.


On Fri, Oct 18, 2013 at 5:08 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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 <jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
>
> ==============================**====================
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-- 
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339