make-namd-restart

pestifer make-namd-restart is a convenient way to generate inputs for sequential NAMD runs, or to complete NAMD runs that terminated early.

For example, say you have a run whose config file was my_run_01.namd and which generated successful output files my_run_01.coor, my_run_01.vel, my_run_01.xsc, etc. Suppose the log file is my_run_01.log. In such a case, we refer to the string my_run_01 as the “basename” of this run; it is also the argument of outputname in a NAMD config. pestifer make-namd-restart can be used to generate the next config file like this:

$ pestifer make-namd-restart --namd-log my_run_01.log --config my_run_01.namd --new-base my_run_02 --run 1000000

This will create the new config file my_run_02.namd and it will specify a run of 1,000,000 timesteps, with inputs comprising the successful outputs defined in my_run_01.namd.

If you are running in a SLURM batch environment, and your SLURM bash script contains an assignment to the variable BASENAME, you can include that as an option to pestifer make-namd-restart and it will update the SLURM script for you; e.g.:

$ pestifer make-namd-restart --namd-log my_run_01.log --config my_run_01.namd --new-base my_run_02 --run 1000000 --slurm my_slurm.sh

This will replace an assignment statement to the variable BASENAME with

BASENAME=my_run_02

If your run terminated prematurely, simply leave off the --run option, and the new config file will be generated with the proper run length to complete the original run as specified.