I'm doing several steps, such as minimization and equilibration, to start running MD simulations and I'm trying to automate this process by running one step after finishing the other. When I go between different steps, I need to provide a PDB file from the last frame of DCD. Is there any way to tell it to write this PDB file within the NAMD configuration file? I've been doing it manually by loading DCD then PSF in VMD and saving the last frame as PDB, which is not ideal for automation.
Right after asking this question, I checked out the commands on this link and tested some out:
https://www.ks.uiuc.edu/Research/namd/2.6/olddocs/ug/node14.html
I was able to write PDB instead of a binary file by adding this line in the first configuration file:
binaryoutput no
Then, giving .coor file as the PDB file to the second configuration file:
coordinates m.coor
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