Is there any way to extract the individual information like Pressure, Energy, Temperature etc from log file of molecular dynamics simulation in NAMD so that I can save them in either .dat format or any other formats to plot it in my favorite plotting tools. I have been using namdplot and saving it in xmgrace format ?
I am not sure about *.log file but If you have *.dcd file, you can convert it into GROMACS formats using python library called MDAnalysis and save a ton of different things including the ones you want.
You can export data from xmgrace to ascii. Alternatively, you can right a small shell script that includes:
grep ^"ENERGY:" logfile | awk '{print $2, $3}' >bond-energy.dat
grep ^"ENERGY:" logfile | awk '{print $2, $4}' >angle-energy.dat
.... and so on
- Badges
- Science topic
- Similar topics
- Phytochemistry
- Extracts