Is there any command, or set of commands, that could be used to completely clear the memory and arrays within in a charmm script. I tried 'dele atoms sele ... end' to clear the PSF, but this alone is not sufficient for my purposes.
In particular, I have a CHARMM script where I do a loop and at the beginning of the loop I add a new atom to the system. At the end of the loop I want to clear everything from CHARMM (e.g., parameters, psf, topology, coordinates) and then be able to read all these files back in again at the start of the loop - the equivalent of restarting CHARMM.
I hope this is possible, as I've been running in to some issues where there are apparently internal structures within CHARMM that are remembering the old system (minus one atom) when I append and add the atom to create the new system. This is leading to some subtle errors in the energy calculation. Wiping Charmm's memory clean should avoid this issue.
I'm using version c35b5.