I have been running steered molecular simulation with NAMD, but in the middle of my simulation it has stopped and i have restarted from specific steps which had stopped. Finally i have two parts of files like dcd, log and etc. Could you help me how can i merge them for forward analyze?
to merge DCD files, you can use VMD or CATDCD Tool. if you are working with CATDCD tool, use this code:
catdcd -o merged.dcd part1.dcd part2.dcd
if you are using VMD, open first part of simulation (PSF, or DCD) , use this code in TK console to load second part:
mol new part1.psf
mol addfile part1.dcd
mol addfile part2.dcd waitfor all
animate write dcd merged.dcd
to merge log files in linux, use this command:
cat part1.log part2.log > merged.log
make sure that time steps or redundant information in the logs do not overlap when concatenating them.
Try doing with catdcd in namd
catdcd -o eq_all.dcd eq01.dcd eq02.dcd eq03.dcd
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