Running¶

Overview¶

The w_run command is used to run weighted ensemble simulations configured <setup> with w_init.

Setting simulation limits¶

Running a simulation¶

Managing data¶

Recovering from errors¶

By default, information about simulation progress is stored in west-JOBID.log (where JOBID refers to the job ID given by the submission engine); any errors will be logged here.

• The error “could not read pcoord from ‘tempfile’: progress coordinate has incorrect shape” may come about from multiple causes; it is possible that the progress coordinate length is incorrectly specified in system.py (self.pcoord_len), or that GROMACS (or whatever simulation package you are using) had an error during the simulation.
• The first case will be obvious by what comes after the message: (XX, YY) (where XX is non-zero), expected (ZZ, GG) (whatever is in system.py). This can be corrected by adjusting system.py.
• In the second case, the progress coordinate length is 0; this indicates that no progress coordinate data exists (null string), which implies that the simulation software did not complete successfully. By default, the simulation package (GROMACS or otherwise) terminal output is stored in a log file inside of seg_logs. Any error that occurred during the actual simulation will be logged here, and can be corrected as needed.