I used mindist of gromacs to find the distance between the proteins (native and mutants) and the metal (metalloprotein) over the simulation period. I have the output in form of graphs.
Is there a way to get the average distance moved?
First of all, you have to create an index file for protein and metal. On the next step you can use the following command: g_dist -f traj.xtc -s topol.tpr -n index.ndx
Hi Thirumal,
If you plot the graph with xmgrace, you can calculate the average distance moved by taking the following steps:
1. Open the graph with xmgrace
2. Click on the Data menu
3. Click on Export and choose Ascii to export the values as Ascii file
4. Use cp linux command to create a copy with .xslx extension
e.g cp AsciFile AsciiFile.xslx. where AsciiFile is the base name of your file.
5. open the file in excel and compute the average
e.g if the cell range of the distance is from b2 to b100, you can calculate the average in another cell as follows: =average(b2:b100), then press Enter or Return key.
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