# Why my analysis plots dont have the typical shapes?

**URL:** <https://gromacs.bioexcel.eu/t/why-my-analysis-plots-dont-have-the-typical-shapes/384>\
**Category:** User discussions\
**Created:** [June 27, 2020, 3:11pm UTC](https://gromacs.bioexcel.eu/t/why-my-analysis-plots-dont-have-the-typical-shapes/384 "2020-06-27T15:11:37Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Azam](https://avatars.discourse-cdn.com/v4/letter/a/ea666f/32.png) [@Azam](https://gromacs.bioexcel.eu/u/Azam)\
**Post date:** [June 27, 2020, 3:11pm UTC](https://gromacs.bioexcel.eu/t/why-my-analysis-plots-dont-have-the-typical-shapes/384/1 "2020-06-27T15:11:37Z")

</div>

GROMACS version:2020  
GROMACS modification: Yes/No  
Hello all. i I have a question about using charmm-gui for input generation in Gromacs simulation.

I downloaded “download.tgz” and used README in the gromacs directory. and run minimization and equilibration steps witout any errors

# step4.0

gmx grompp -f step4.0\_minimization.mdp -o step4.0\_minimization.tpr -c step3\_input.gro -r step3\_input.gro -p topol.top -maxwarn 1  
gmx\_d mdrun -v -deffnm step4.0\_minimization

# Equilibration

# step4.1

gmx grompp -f step4.1\_equilibration.mdp -o step4.1\_equilibration.tpr -c step4.0\_minimization.gro -r step3\_input.gro -p topol.top  
gmx mdrun -v -deffnm step4.1\_equilibration

_but instead of_ this

# Production

set cnt = 1  
set cntmax = 10

while ( {cnt} \<= {cntmax} )  
if ( {cnt} == 1 ) then gmx grompp -f step5\_production.mdp -o step5\_{cnt}.tpr -c step4.1\_equilibration.gro -p topol.top  
gmx mdrun -v -deffnm step5\_{cnt} else @ pcnt = {cnt} - 1  
gmx grompp -f step5\_production.mdp -o step5\_{cnt}.tpr -c step5\_{pcnt}.gro -t step5\_{pcnt}.cpt -p topol.top gmx mdrun -v -deffnm step5\_{cnt}

i run the production step for 1 nanosecond using these command lines:

gmx grompp -f step5\_production.mdp -o step5.tpr -c step4.1\_equilibration.gro -p topol.top  
gmx mdrun -v -deffnm step5

but when analysing the data i noticed that the resulting plots for gyration redius(Rg), rmsd,rmsf ,… have not the typical shapes .so i guessing the problem is the setting in production.mdp file.  
In fact when opening the rmsd.xvg, gyrate.xvg , rmsf-res.xvg,…plots in excel programm  
there is just 10 points,while this plots shoud be have abut 100 points , so the plots have not a proper shape.  
[rmsd.xvg](https://gromacs.bioexcel.eu/uploads/short-url/x45vZnXpJm6bwURG6I3tOY8e8WC.xvg) (880 Bytes) I dont know how resolve this problem. can i change some settings in mdp file to achive a typical plot?  
I have attached an rmsd.xvg .Please let me know how overcome this problems . Any help is appreciate

Best whishes

Azam