[gmx-users] Density calculation

Md. Imrul Reza Shishir imrul.reza.shishir at gmail.com
Wed Apr 12 03:27:06 CEST 2017

Dear all
I want to calculate the density of cellulose fibril. My simulation system
is cellulose in a box of water and ions.

If i apply "gmx energy" after NPT simulation then i will get density of
total system which is lower than what expected because of water.

"gmx energy -f *.edr -s *.tpr -o density.xvg " select the group density

If i use "gmx density", i get the density distribution along a axis.

"gmx density -f *.xtc -s *.tpr -o density.xvg " select the group of atom

So, how i will get the density of selected group as an average of time
period or distribution.

​Thanks in advance.​

​ ​
*Md Imrul Reza Shishir*
Master Student
*Inha University*

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